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<property name="body"><![CDATA[h1. Items


h4. &nbsp;Tech Transfer

* &nbsp;Cheri here working with getting NOAA machine running.&nbsp; Roman has identified many issues:
** &nbsp;deepened o-ring groove on heaters
** tightened carousel bearing reatiner
** loc-tite outside of bearing
* room temp calibrations now finsihed; enviro chamber next for hi/lo temps
* ESP Chris has same flaws.&nbsp; Cheri will be responsible for redoing these.

h4. Drifter

* &nbsp;Sea test is August 11 on Shana Rae.
* Will be using ESP-Bruce.&nbsp; Today hand and carousel calibrated.&nbsp; Check waste tomorrow.&nbsp; Array prints look good.
* Must check with Kevin on whether GUI will work on Kilo Moana in order to view data.

h4. HAB/Cybr Assay

* &nbsp;Elif is getting cross-reactivity with non-targets on the ABI.&nbsp; Also having some problems with MFB5.
* Now concentrating on TAQ assay.&nbsp; moved primers a little but still cross-reactivity.&nbsp; Will continue tweaking Taq assay.&nbsp; Remember ultimate goal(s):
** Want to do PCR for P. australis in ordre to
** compare SHA and PCR results.

h4.


h4. Pier Deployment

* NEO is going on Pier.&nbsp; Mid/late October.&nbsp; Chris working on upgrading everything and getting regular MFB (not tombstone) working.\\ \\]]></property>
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<property name="body"><![CDATA[h2.


h1. We currently (Apr-2015) have three Melo trackers

{color:#006600}The Melo is the 'watch-circle' warning transponder for surface moorings.{color}\\

IMEI numbers:

h3. *300034012090780&nbsp; (purchased June, 2011)*


h3. 300234060016190&nbsp; (serial # 122)&nbsp;&nbsp; (both purchased Dec, 2012)


h3. 300234060014550 (serial # 123)


h2.

(IEMI number for Sable 5000 on D-ESP:&nbsp; 300034012099780)

h1.

User's Manuals
# [Quick Start Guide v1.2|^Xeos_Melo_manual-1.pdf|quick start]
# [User Manual v1.5|^Melo_User_Manual _watch_circle_V1.5.pdf|Full Manual]
# [Watch Circle Console User Manual v2.1|^Xeos_Melo_manual-3.pdf|watch circle]\\
# [Xeos pricing changes as of Jan 2013|^Xeos_Iridium_BillingProcess_CustomerLetter.pdf]]]></property>
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<property name="body"><![CDATA[This page details out the data model that exists in the database to back the object model.
!data model.jpg|align=centre!

h2. Notes

* I've written a basic CRUD test so I know that it can insert and delete trees of objects. Beyond that we'll have to work things out.
* At this point there is NO business logic implemented.  If a transaction breaks some database rule, for example, trying to insert a ConsumableAmount without a ConsumableType, an Exception will be thrown.
* Collections are lazy loaded but I haven't written any unit tests to verify that they're working.
* I had some issues with the ConsumableAmount table. It's a many-to-many join table with an extra column for storing a value. JPA *hates* that. (You have to have the primary keys for both the ConsumableType and PhaseType *BEFORE* inserting the ConsumableAmount; so ConsumableAmount would've need to be handled is separate transactions.) The workaround was to add an id column; it's not pretty but it works.
* All testing has been done against FOG. Is this copacetic or should I start setting up MySQL for developing against?
* All transactions are currently handled through a single EAO object.
* The ESP-DAL (<\- Data Access Layer) build uses Maven 2. A dependency graph is available at [here | ^ESP - Data Model Dependencies.png]

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# Kevin Gomes
# Chris Scholin
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# Scott McLean
# Jim Birch
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# [WBS and Costs (xls)|ESPAPP:ProjectPresentations^PDR.xls|WBS Spreadsheet]
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<property name="body"><![CDATA[h3. Minutes
{section}
{column:width=60%}
# Phases: HAB, BAC, LARV
# Phases run protocols
# Phase is a series of operations (could be one protocol, but more likely more).  Can be one puck, but more likely more.
# Phase is a standard set of operations
# Each protocol needs a puck (with filter)
# Filter may or may not have probes, whole cell has no probes, just brings home sample
# All pucks have serial numbers.
# pucks outer diameter is the same.
# there are different pucks for different
# SH = standard hybridization, detect molecules of interest. Heat it up and liquify.  Filter and then apply to SH2.  SH1 pucks can be used lysate.
# Why do we want to keep track of serial numbers on pucks
# Once puck is closed, not sure what is in there.
# Serial numbers help keep track of what they intend to use it for after build.
# Some have physical specimen and they need to figure out which puck has the specimen
# After filteration, put on another filter, then more chemistry, then image.
# Final PUCK is WCR (whole cell archival) is then sample is then preserved and brought home for shore side analysis
# Associated with probes is spot map (array map) ".Gal File" (what probe in what X,Y location).  Often listed as "Spot 23" then lookup with tell you X,Y
# Image is analyzed and you get intensities.
# Device can do "auto exposure" to figure out where it needs to be to get image in linear range of CCD chip.
# Also ask for constant exposure (do more than one constant exposure).
# Use standard curves and control spots on map.
# Standard curve is number of bugs/intensity
# Run exposure that you have standard curve for and then get intensity which then you lookup on the spot map.
# Low res images come across the wire (high res is 1MB).
# Phases can change the protocols (should we force users to use unique names- Chris thinks this would be good)
# Array map evolves.
# Protocols use same reagants, same amount 
# Phase-protocol combination (Phase tells you what the amounts are in the different protocols)
# Volumes filtered varies (tell it "Collect a liter", instrument decides how much until to filter until clogged)
# Print info comes from "gal file".  Old print is excel file.
# Some filters are thrown away, some are archived.
# Comments also need to be captured.
# Events are "when we sample"
# User specifies start of phase
## Then delay (7 minutes let's say), then sample is taken (that is the actual "start").  The rest of the protocols depend on the environmental characteristics.
# There will be maximum time for each phase (can be shorter, never longer).
# Instrument capacities:
## Pucks: 
## Reagants: 20
## Waste: fixed in current machine
# Configuration file tells what reagents are at what valve.
# There is a waste 1 and waste 2 (NOTE this is dependent on the reagent. specify which waste reagent goes to)
# Power budget.
# Instrument run
## Take series of protocol, to build phases
## write high level script
## derive max volumes.
# Number of pucks is usual limitation
# sometimes waste can be limiter.
{column}
{column:width=40%}
{panel:title=Attendees}
# Chris Scholin
# Rich Schramm
# Brian Schlining
# Karen Salamy
# Kevin Gomes
{panel}
{column}
{section}

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<property name="body"><![CDATA[Present:&nbsp;&nbsp; Brent, Jim, Scott, Chris S.

Absent: everyone else....
\\

h2. &nbsp;Issues:

McLane joined us via phone for first part of meeting.
* Learned that host board we sent was only 8MB, and would not work for them.&nbsp; Although we typically use 16MB boards, the smaller boards should have worked.&nbsp; They are ordering 16MB board and will have it shipped to us.&nbsp; Brent to check it out.
* Camera issues.&nbsp; New cameras have pixel shift in bottom 2-3 rows of pixels.&nbsp; powering on/off usually removes this.&nbsp; Much more testing needs to be done to approve the newer cameras.&nbsp; MBARI (Brent) will do this testing, to begin as soon as we receive the host board from them.&nbsp; Scott has ideas on how to supply 12V power to the newer cameras.&nbsp; Once we get the board, anticipate 1 week of testing.
* We'd like to piggy-back on the temperature sensor board order McLane is about to make.&nbsp; Order 10 boards; 5 stuffed, 5 PCB's.&nbsp; Also 20 backing mounts for these boards.
* We will notify Ivory of the blue-wire fix for the ESD problem Scott discovered on Betty.

h5. +Machines+


h6. Bruce

Has new firmware, but there are issues with calibration.&nbsp; Tina using currently--will try and squeeze in b/w her runs and recalibrate (Scott).

h6. Mack

currently on Drifter.&nbsp; Just learned it has loose PSV, and was blowing out WCR, so nothing collected.&nbsp; Still needs firmware update.

h6. MOE

&nbsp;has latest firmware (v3.7).

still has pressure issues--several issues:\* pressure gauge changes over time; possible PEEK creep causing it.&nbsp; we will turn down gain to increase the head space of the gauges
* snap pucks come apart
** clamp isn't strong enough.&nbsp; Scott to talk to Doug about spring change.&nbsp; Also will run clamp w/heat to see if PEEK changes more.

h6. NEO

currently in water at M0. will get latest firmware when recovered (Aug 30)

Must decide what Science wants to do with NEO.&nbsp; Will there be a pier deployment in Oct/Nov, and do we rid NEO of the tombstone and replace with an MFB and the attendant firmware upgrades, so all cores will be running the same thing?&nbsp; Discuss this at next Tuesday's science mtg.

h6. Gordon

Still in the ball.&nbsp; Chris P. hopes to be finished with post-cruise QC runs by Monday.

h6. Betty

still not ready for science checkout.&nbsp; Pressure issues among others.

h3. Communications for BIOSPACE

&nbsp;Question is whether one antenna on Brent's house can hit both the bight and the shadow ESP position.&nbsp; Plan is for him to get a wider angle antenna (not omni) and shoot it down the middle, or almost so, and try and hit both positions.&nbsp; Has a sailing friend who heads out every Weds who can take some radio gear and go to each GPS coordinate and see if Brent can ping the boat from his home.

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# [Engineering Meetings]
# [Software Development Meetings]]]></property>
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# [Opening in an IDE]
# [Image Processing]
# GUI Notes
## [Ruby integration]]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]
# [Feb 16]
# Feb 23 \-\- Oceans Mtg., Portland
# [Mar 2]
# [Mar 9]
# Mar 16 \-\- Jim in S. Cal scouting.  John Ryan ran mtg.
# Mar 23
# Mar 30
# Apr 6 \-\- canceled in preparation for M0 deployment
# Apr 13
# Apr 20
# Apr 27 \--AbSciCon, League City TX
# [May 4]
# [May 11]
# [May 18]
# [Aug 24]
# [Sep 14]
# [Sep 21]
# Sep 28 \-\- Network deployment.&nbsp; no mtg
# Oct 5
# Oct 12
# Oct 19
# Oct 26 \-\- Chris S. @ WHOI, Jim at PICES
# [Nov 2]
# [Nov 9]
# [Nov 30] \--Year re-cap
# [Dec 7] \--&nbsp; Julie gives project update; Bill shows AGU poster draft]]></property>
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h3. Eclipse
# [Check out the esp/trunk from SVN|http://kahuna.shore.mbari.org/viewvc/esp/trunk/]
# cd to the directory you checked it out to
# In a terminal run: {code}mvn eclipse:eclipse{code}
# In eclipse do _File->import_
#* Select _existing project from workspace_


h3. IntelliJ IDEA
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# cd to the directory you checked it out to
# In a terminal run: {code}mvn idea:idea{code}
# Do _File->Open Project_

h3. JBuilder
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# In Jbuilder do _File->import_
# Select _existing maven project from workspace_

h3. Netbeans
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# Install the Maven plug-in in Netbeans
## Select _Tools-Plugins_
## In the dialog that appears, select the _New Plugins_ tab
## Check the box next to *Maven*
## Press the install button
# Do _File->Open Project_
# Select the project (Netbeans will open all the child projects too)
]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Doug P, Chris S, Chris P, John R, Brent, Bill

h3. General

* &nbsp;Be sure to check out the fantastic job Kim FB is doing on the CMORE Drifter Blog.
* Kelly Lincetum from ASU may be coming out next week to go on the Zephyr and collect water.&nbsp; ASU needs 'background' and this would give them a window into foundational oceanography, and perhaps give a better appreciation of sampling issues as it relates to their PCR efforts.&nbsp; We may have a big 'filter-fest' and save some for us.

h3. ESP User Group Meeting (Sep 27-29, 2011)

* This meeting will discuss G2 items only.
* Chris S will give high-level overview.&nbsp; John R high level overview of L+O paper and BloomX update.&nbsp; Chris P high level PCR (not water quality)
* MBARI is finished at 1:30 on Tuesday, although there is an afternoon session Weds afternoon at Spyglass.&nbsp; May have Chris p, Bill, Doug attend and talk about pier stuff.
* We will suggest shortening the panel discussion Tuesday at MBARI and make room for Brent to talk about comms. (Jim to contact Spyglass)
* Also suggest moving Kevin's GUI discussion to earlier.
* &nbsp;Spyglass needs arrays for this meeting.&nbsp; We do not have.&nbsp; They should contact WHOI.
* Will email Melancon/Shana a copy of the Nov, 2009 Fluidics path diagram.

h3. Core

* Pier deployment on schedule for Friday, October 14.&nbsp; Will wait until Roman returns Sep 26 to start pinging Pier guys for access to set-up radios
* Latest SW changes for combined array/PCR have introduced very BIG script changes.&nbsp; These changes will need to be pushed out to the upcoming users who want to do both PCR and SHA.

h3. G3 Development

* Functional Requirements document has been updated and sent out to team for comment.  Please return comments by end of week and Jim will incorporate.  Req's document will be kept on Confluence with date stamps so most recent will be easy to find.
* Some confusion about what separates the 'Sampler' module and 'core' module (analytical module seems well-defined).  Some effort needs to be expended to define the Sampler a little better.
* This new 3-box division (sampler, core, analytical module) makes some sense with regards to breaking up labor, but careful attention needs to be paid to the where the 'fences' are between boxes and subsequent effects on requirements so each box will play well with its downstream neighbor.]]></property>
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<property name="body"><![CDATA[h2. Below are links to attached Word Documents

# [Spring 2010|^ESP G3 project overview.doc|first pass FR for G3]
# [Nov 11, 2010|^ESP G3 project requirements.doc|second pass FR for G3]
# [Sep 15, 2011|^Funct Req Sept 15 2011.docx|third pass FR for G3]
# [Sep 21, 2011|^Funct Req Sept 21 2011.docx|fourth pass FR for G3] updated after 9-21-2011 group meeting.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Scholin, Robidart, Marin, Ryan, Birch

1.&nbsp; Discussed January schedule of all people.

2.&nbsp; Probe inventory; Roman would look into.

3.&nbsp; Discussion of papers to publish

4.&nbsp; Dry-run of MTC reagent production will be week of Jan 18.

5.&nbsp; Discussion of CMORE meeting (Feb. 1).&nbsp; Must give poster (Julie) and will ship an MFB.&nbsp; Will print-out and bind several MFB manuals (Jim).&nbsp; ]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab'. NOTE: The color selector was used in an older version to display on the calendar but is no longer used and will be removed in the future, you can ignore the color chooser.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse over the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For this reason, we don't allow spaces in mission names.  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/15/2011 00:00:00 |
| End Date | The date at which the mission will end | 8/31/2011 00:00:00 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | ftp.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://ftp.mbari.org/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_ which means the host is _ftp.mbari.org_ and the FTP Root is _/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|align=centre!
# What you now see is a small calendar icon in the upper portion of the colored mission bar on the calendar.  It is place at the top of the mission bar to indicate that it is a planned protocol, not one that was extracted from the log file (which you will see later).  Also, the small pencil on the icon means that it is a planned protocol, not an actual one.  The small letter at the front of the icon is used to help distinguish the which protocol this is.  It is simply the first letter of the name that you gave the protocol.  You will alos notice the list of "Planned" protocols in the lower left pane shows the list of protocols you have planned so far.  I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the Protocol, Event and Data Window.  As mentioned above, the first tab "Planned" shows you the protocols that have been planned for this mission (what you created earlier). You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Images", "Errors" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates (which we will do shortly).  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the files are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take a while to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
!ESPGUIFigure23.jpg|align=centre!
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
!ESPGUIFigure24.jpg|align=centre!
A window will open showing you the progress of the log file parsing.
!ESPGUIFigure25.jpg|align=centre!
Once the log interpretation is complete, you should see many more things in the calendar view.  In the figure below you will notice several new things.  The exclamation points in the middle of the mission bar on the calendar indicate an error during the run of the ESP and the calendar icons with green arrows at the bottom of the mission bar indicate protocols that were found in the log file.
!ESPGUIFigure26.jpg|align=centre!
At this point, we can begin to explore some information about the currently deployed ESP.  If you select the "Actual" tab in the lower left pane, you will see the list of protocols that were interpreted from the log file.  You see the name of the protocol, the start date and time, the target/actual volumes of the associated water sample and the difference between the target and actual (if there is one).
!ESPGUIFigure27.jpg|align=centre!
If you click on the protocol either in the calendar view or in the "Actual" table, you will see more details about the protocol in both the Protocol Graph Window and in the Context Sensitive Details Window.  In the following figure, I selected the first pcr protocol.
!ESPGUIFigure28.jpg|align=centre!
In the Protocol Graph Window you can see some details about the various related artifacts.  In this example, since this if from the Deep ESP, you can see that the water sample associated with the PCR itself was extracted from a DWSM sample.  You can also see the associated images that were taken of the analyzed sample associated with the PCR.  The WCR that is show gives you the information that there was indeed an archive performed in association with this PCR. In the context sensitive details window on the lower right side of the screen you can see the entry in the log file that the PCR protocol was extracted from.  If you select one of the images in the graph or switch to the "Images" tab, you will get more information about the image you have selected.
!ESPGUIFigure29.jpg|align=centre!
The image tab shows a table with some information about the selected image such as the date and time it was taken and the exposure that was used.  In the context sensitive details panel, you can see the image itself and if you select the "Metadata" tab you will see the information extracted from the TIFF image itself.  The "Log Entry" tab shows the location in the log file that this entry was extracted from.  Next if you select an Error exclamation point in the calendar view, or switch to the "Error" tab, you will get more information about the errors that were discovered in the log file.
!ESPGUIFigure30.jpg|align=centre!
In this example, you can see the error is the abort of the mission and when that error occurred.  In the context details window, you can see the log entry with a window of lines on both sides of the entry so you can see the context in which the error occurred. If you select the "Ancillary" tab, you can get information about the ancillary data that was extracted from the log file.  This is the data the is logged by sensors in the ESP itself in addition to other contextual sensors that are attached to the ESP and are logging their data through the ESP. In the example shown below, there is data available from the ESP Can itself as well as from an associated CTD and an ISUS.  If you select an appropriate time window (for this example, I chose Jul 17 through July 20, then choose the variables you are interested in and click "Refresh", you will see a plot of the various data in the context sensitive details window.
!ESPGUIFigure31.jpg|align=centre!
If you right-click on the plot itself, you will be presented with some options to save, print or zoom/pan the ancillary data plots.  
!ESPGUIFigure32.jpg|align=centre!
If you want to save the data that you have plotted, in the left window, click on the "Save Selected" button and it will present you with a file dialog so you can save a comma separated list of data points to your disk somewhere for further analysis. Note that in the resulting CSV file, the dates and times of the different data do not align and so where there is not data "N/A"s are inserted as excel understands those as no data.

Another thing that may be helpful, is that if you select on the "Files" tab again, and if there are any files that are PCR results (i.e. end in .pcr), you can select those to see plots and tables of the data in the PCR results file in the context sensitive details window.
!ESPGUIFigure33.jpg|align=centre!
Lastly, if you are interested in a CSV formatted file of the information from the ESP mission, you can right-click on the mission in the calendar view and select "Export to CVS File" which will give you a dialog box to save a CSV formatted file with some of the information from the mission to date to your computer.
!ESPGUIFigure34.jpg|align=centre!
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{quote}

h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound (33.799, \-118.647).

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deployment-MOE @ M0-\- w/PCR, ISUS.&nbsp; 121 54.11 E; 36 50.10 N.&nbsp; 72m water depth
{color:#33cc00}September 29{color} \-\- Bruce @ offshore (SC) with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; 36 53.75&nbsp; \-122 2.75. 52m water depth.&nbsp; Weight measurements are [HERE|ESPAPP:Weight Calculations for BRUCE|mooring weights].
{color:#33ff00}September 28{color} \-\- Mack @ bight \--&nbsp; no ISUS. no PCR; Using RNALater as preservative.&nbsp; 36 55.95&nbsp; \-121 55.35.&nbsp; 19m water depth.&nbsp; (Lat/Long are from Aaron Gregg after deployment.)

{color:#00cc00}Nov 3{color} \-\- recover all three.  Moe ran out of battery on/around Oct 28.
\\

{color:#ff6666}Nov 30{color} \-\- Deploy D-ESP on MARS.&nbsp; Gordon w/ PCR.&nbsp; Reagents/mission for 2 month deployment.
\\
{quote}

{quote}Dec 2 (4pm) lost network connectivity. 48V current went from 3A to 0A; isolation relay triggered, cutting off ethernet.&nbsp; 375V continues powering heater.
Dec 6 \-\- 375V current has dropped to zero.&nbsp; Ball is dead.
Dec 8 \-\- 10:30am, somehow ESPMars rebooted.&nbsp; temp 5.5C when rebooted.

Dec 9 \-\- 2:30pm.&nbsp; Restarted mission.
\\

Dec 23 \-\- lost communications soon after 6:20pm.&nbsp; 375V stopped drawing on Dec 28.\\ {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS
\\
\\
\\
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<property name="body"><![CDATA[h3. Quick Science Meeting

# &nbsp;Noted that pucks seem to be 'denting' on top and leaving o-ring impressions.&nbsp; This was after JdF cruise.&nbsp; We need to do some forensics on where these impressions are coming from.&nbsp; Single o-ring may be concentrating force in middle of puck and 'denting'.&nbsp; (later discussions make this unlikely; Doug says Ti is too stiff, and only compression is of o-ring, then entire clamp face is holding puck.)&nbsp; Bill has measured some pucks, and found irregularities, but engineering does not think findings are significant.
# HAB/SHA testing (Elif)
## we are testing cultures for contamination
## Elif has created flow-charts for what needs to be done next (she will have child any day now...)
## She'll organize her standards and primers.&nbsp; Still working on specificity of primers.
# Bill and column testing
## has Global-FIA columns and wants to test various column material (silica vs. hydroxyapatite)&nbsp;
# CTD is ready for Drifter.&nbsp; Will clean deep CTD.

Will have a 'lessons learned' meeting in Sept, regarding flooding of ISUS.
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\\
# Will send MELO notifications to jrobidart@gmail.com and to esp001@mbari.org
# Sea-test on Aug 11 on Shana Rae.&nbsp; (This subsequently got moved to Aug 12).
# Working in van will require constant hearing protection
# Travel.&nbsp; EVERYTHING goes through Annette.&nbsp; Deployment will be charged to 708602.05
\\]]></property>
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# &nbsp;For 5 NIF genes have good standard curves for 4 of the 5.&nbsp; Won't use Gama Proteobacteria as these had poor standard curve.
# Column on MOE has been changed.&nbsp; Don't know if leaving the column in after 1 or 2 uses is detrimental.&nbsp; Will bring extra columns to Hawaii.
# Remaining task is to load reagents.&nbsp; Archiving at 5um and 0.2um.
# Must check with Chris P to see whether the planned archive/PCR is correct, as far as waste generation is concerned.
# check with Scott regarding power budget.&nbsp; Jose is organizing ESP batteries.
# Roman and CTD:
## has fresh batteries
## calibrated for blue ocean water
# Once recovered, get ADCP, CTD, PAR sensor data off so we have a copy incase we lose instrument.
# Will have HOBO temp logger going and returning.
# will use Mack for end-to-end testing on Aug 11 Shana Rae test day.
# Con-Ops
## We want to be near a convergetn front, far enough away to get similar water, THEN run in/through the front.
## Whether to recover and move it, or simply tow it needs to be decided on the fly.
## Mission will be real-time run for first 3 days (archive and PCR) then slow down the archives and continue PCR.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris P., Doug, Brent, Jim, Scott, Cheri, Julie

Absent: Chris S., Roman
\\

h2. &nbsp;Issues:

1.&nbsp; NONE\!

h2. Methane cruise

1.&nbsp; Discussion of what to do if Flyer is out of service.&nbsp; Currently out for month of June to rebuild one engine.&nbsp; Also issue is what if ROV is not usable?&nbsp; We will continue moving forward, as though the deployment will take place, although contingencies will be developed should problems arise.&nbsp; Decision should be made as early as possible in order for people to plan their vacations.

2.&nbsp; Bag limit-switch will be set-up tomorrow.&nbsp; Chris P. starting core testing of Gordon tonight.&nbsp; the MFB run through the standards will take through this weekend.&nbsp; SPE column still needs changing, and Chris to do that Sunday.&nbsp; Will meet with Scholin tomorrow (Friday) to discuss various chemistry issues that Chris P. has been exploring.&nbsp; Chris P. will lean on Julie if/when she needs help.

3.&nbsp; Pressure testing of DWSM is going well.&nbsp; It has been tested to 1600psi and all connections look good.

4.&nbsp; Julie brought up issue that Luke mentioned that our bleach solution in DWSM may have been causing spurious ISUS readings.&nbsp; Discussion was directed at conversing with Luke about how the way we use bleach could not have given the readings ISUS gave.

5.&nbsp; Mass Spec has checked out visually.&nbsp; Wayne to fire it up early next week, and we will mount it in its pressure housing (which has arrived and resides in shipping), and perform dunk test late next week.

6.&nbsp; Modem deck box arrived and it turns on(\!).&nbsp; Cables to connect modem are still being made.&nbsp; Discussion ensued over testing just that much of it to make sure it worked the burn wire/drop wt release mechanism, or wait until we got everything together to test.&nbsp; If we wait, and it needs to get sent back to Benthos, we may not have time.&nbsp; We will check this out next week to ascertain how much time/work it will take to do the complete test vs. a short test.

h2. M0 Flip

1. The 'hot-swap' of can and batteries onto the existing surface mooring went very smoothly on Tuesday.&nbsp; MOE is in the high bay now running through it's post-deployment QC.&nbsp; Next flip is scheduled for June 15, and much discussion about moving the next flip date back a week to give Julie more prep time.&nbsp; We must remain cognizant of our power limitations (unlikely we will make it beyond 4 weeks, running PCR).&nbsp; Jim will talk to Grech next week and see what the likelihood of moving our dates will be.

2.&nbsp; Short discussion about keeping the high-bay clean.&nbsp; We all know that...]]></property>
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<property name="body"><![CDATA[These are some notes about the servo model design and implementation.

Here are some of the plots generated from the unit tests:

| !test_similar_to_servoTest.png!  |  !test_absMoves_with_direction_change_before_stop.png! | 
| !test_setRawLimits_and_abrupt_stop_overCurrent.png!  | !test_getTimesForLimits.png!    | 
| !test_CompositeFunction_simple.png!                       | 

h1. Design in a nutshell

At time of writing the code resides in the 'servomodel' branch:
   https://github.com/MBARI-ESP/ESP2Gscript/tree/servomodel

The main source file, where the {{I2C::Servo::Model}} class is defined is: [servomodel.rb|https://github.com/MBARI-ESP/ESP2Gscript/blob/b63f5de300c96e1d2e1f68f7ac13eab01fa3e7f5/lib/i2c/model/servomodel.rb].

The servo simulation is modularized in a layered way. Elements of the modeling itself are under the {{ServoModeling}} module:

- {{Servo::Model}} and related elements are only concerned, in terms of the characterization of the velocity-position function, with {{ServoChannelSimulator}}.

- {{ServoChannelSimulator}} makes use of a {{FunctionFactory}} to keep and adjust the overall velocity-position function according to move commands.

- {{FunctionFactory}} facilitates the construction of {{Function}}'s.

- Possible {{Function}}'s are:
-- {{ConstantFunction}}: function always evaluating to {{\[0, pos\]}} for a given position
-- {{MonotoneFunction}}: captures the basic velocity profile of starting at a given velocity, and then going through acceleration, plateau (each of which can be of zero duration), and deceleration zones. Starting at a given initial position, this function changes the position monotonically in a given direction.
-- {{CompositeFunction}}: function composed of the concatenation of multiple functions, each applied from a specific time wrt the previous one.


h1. Testing

h2. Unit tests

All unit tests can be run at the command line as follows:

{code}
$ find test/lib/i2c/model -name \*_test.rb -exec ruby -I. -Ilib -Iutils -Itest/lib {} \;
Loaded suite test/lib/i2c/model/servo/function_test
Started
..........
Finished in 0.013645 seconds.

10 tests, 607 assertions, 0 failures, 0 errors
Loaded suite test/lib/i2c/model/servo/functionfact_test
Started
..........
Finished in 0.029115 seconds.

10 tests, 1068 assertions, 0 failures, 0 errors
Loaded suite test/lib/i2c/model/servo/servochannelsim_test
Started
.......
Finished in 0.08877 seconds.

7 tests, 2531 assertions, 0 failures, 0 errors
Loaded suite test/lib/i2c/model/servomodel_test
Started
.......
Finished in 0.188708 seconds.

7 tests, 184 assertions, 0 failures, 0 errors
{code}

h2. Test with actual integration in the framework

The following tested in both {{simfast}} and {{simreal}} modes:

{code}
carueda@bufflehead:~/esp2$ . bin/ESPenv shallow moe
carueda@bufflehead:~/esp2$ ESPmode=simfast
carueda@bufflehead:~/esp2$ esp
ESPmoe:001:0-> require 'plot'
true
ESPmoe:002:0-> ssLog = SS.log {SS.home.empty; SS.fill}
SS.reconfigure SSconfig
SS.home.seek empty
@16:00:00.82 SS.seek 25.00ml
[<I2C::Servo::Status enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=-12, velocity=-12, current=0, pwm=0, err=0, inPress=0, outPress=0, deltaPress=0, voltage=12.1620363279332>,
...
 <I2C::Servo::Status enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=108084, velocity=12, current=0, pwm=0, err=0, inPress=0, outPress=0, deltaPress=0, voltage=12.1620363279332>,
 <I2C::Servo::Status enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=108096, velocity=0, current=0, pwm=0, err=0, inPress=0, outPress=0, deltaPress=0, voltage=12.1620363279332>]
ESPmoe:003:0-> plot ssLog
#<Thread::PLOT_1 priority=1 sleep>
ESPmoe:004:0->
{code}

The generated plot:
!servosim-quickplot-1.png!

Some other commands:

{code}
@09:23:13.98 -> SS.status
#<struct I2C::Servo::Status enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=108096, velocity=0, current=0, pwm=0, err=0, inPress=0, outPress=0, deltaPress=0, voltage=12.1620363279332>
@09:23:18.32 -> SS.goal

@09:23:25.46 -> SS.getConfig
#<struct I2C::Servo::Configuration samplePeriod=1, encoder=:negative, threshold=:off, home=:negative, jogHome=false, homeDirection=false, thresholdOffset=0, maxPositionErr=1000, stopWindow=6, gain=#<struct PIDgain P=400, I=12000, D=1000>, acceleration=6, deceleration=0, stopRate=0, maxSpeed=150, minSpeed=15, maxPWM=98, minPWM=-98, maxSettling=64, maxCurrent=600, stiction=5, friction=60, hunt=true, brake=true, maxDeltaPress=false, maxInPress=0, maxOutPress=0, minDeltaPress=false, minInPress=0, minOutPress=0, pressBias=0, pressGain=0, inputDeltaPress=false, externalCurrent=false, debug=false>

@09:24:30.19 -> SS.setPosition! 2
SS.setPosition! 2.00ml
Sampler Syringe at 2.00ml
@09:24:35.31 -> SS.status
#<struct I2C::Servo::Status enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=5472, velocity=0, current=0, pwm=0, err=0, inPress=0, outPress=0, deltaPress=0, voltage=12.1620363279332>

@09:25:03.46 -> SS.jog -3000
SS.jog -3000
Sampler Syringe at 1.33ml

@09:25:29.29 -> SS.status
#<struct I2C::Servo::Status enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=2472, velocity=0, current=0, pwm=0, err=0, inPress=0, outPress=0, deltaPress=0, voltage=12.1620363279332>

@09:25:50.72 -> SS.to 5
@09:25:50.73 SS.seek 5.00ml
Sampler Syringe at 5.00ml
@09:25:54.42 -> SS.status
#<struct I2C::Servo::Status enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=18858, velocity=0, current=0, pwm=0, err=0, inPress=0, outPress=0, deltaPress=0, voltage=12.1620363279332>

{code}
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<property name="body"><![CDATA[Doug will be on vacation July 14-July 28.
Scott will be on vacation July 16-July 22.

h2.

present:  Chris S, Addie, Cheri, Brent, Jim

h3. Instrument Builds

* Decision to make NEO the PCR machine, as Moe will not be ready in time.&nbsp; Cheri is working on converting Moe to make it PCR-enabled.
* {color:#660000}Must remember that Mack and Bruce are still using back-side puck temp sensors. Neo has been changed to front, as should these two eventually.{color}

h3. MFB

* Brent commented that much code has been checked in, but not OUT, so still lots of integration needed.
* Changing the SPE column has successfully knocked down the signal on the negative runs.
* Addie continues to build the grill; waiting on ball screw and syringe pieces from Mike
* Check valves have arrived.&nbsp; Idea is to reduced back-flow from pressure difference flows; this may be a big change in scripts and build, so tabling this change now.&nbsp;

h3. Software

* New firmware is working, but still needs minor amount of testing.&nbsp; Intended to install on Moe (w/PCR), but now decision is NO FIRMWARE changes until DWSM comes online.
* Brent looking into 2 ESP's at M0 w/ only 1 shore radio.
* GUI Development
** need to assess 2009 needs
** Will mt with Kevin, Rich Schramm, Jim B, Chris S., Brent
* Scoping of S. Cal Piers still in planning stage.
h3.


h3.


h3. Other Items

* Chris S. asked about building a 3rd surface mooring.&nbsp; Will talk to Mark Brown.&nbsp; Idea is to have 2 machines at M0, 1 at Santa Cruz.&nbsp; Jim looked into this and it is possible.&nbsp; Jim Scholfield will work on starting July 22.
* McLane visits next week (Wed/Thurs).&nbsp; Weds will be tech discussion, Thursday will be business discussion.
* SFWD rep (Mike Casteel) visits today to discuss collaboration of ESP in SF municipal water monitoring.]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 17, 2008*

*11am-12*
Present: Jim, Doug, Addie, Scott, Cheri, Brent, Kevin

h3. Tech Transfer


h6. Discussion Items:

* Arm status update
* Environmental test chamber update

*Arm/Hand*.&nbsp; Removed Bruce from cold testing, and _almost_ finished with hand cold testing.&nbsp; Removed hand from Bruce and installed on Mack. Plan is to finish cold-test on hand and cold-test valves simultaneously on Mack.&nbsp; First priority in cold is to finish testing hand gripper.&nbsp; Once it passes, Mike will get green-light parts of the other hands (first 3 old action items).&nbsp; Order is placed with Maxxon for new forearm motors (maybe 6-8 weeks).&nbsp; Small order of fluidic fittings still needed for all of them.&nbsp; (Cheri)

*ETC* (Environmental Test Chamber).&nbsp; Cold box finished, electrical connectors in, fluidic connectors still need to be put in.&nbsp; New rotary valves all on Mack and being homed and calibrated.&nbsp; All we be ready for cold testing by end of day.

+Action Items+

ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp;

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}
{color:#000000}ACTION:{color}&nbsp; cannot purchase on 708 grant yet.&nbsp; 701312.04 should take all cost.&nbsp; Change:&nbsp; Order only 2 cans (Jim):&nbsp; {color:#0000ff}DONE; ordered 1-11-08{color}
ACTION:&nbsp; talk to Jose to figure a solution to broken home sensor cable. (Scott/Doug/Cheri){color}&nbsp;{color} {color:#0000ff}DONE{color}
{color}ACTION:&nbsp; Contact MAXON about forearm motors (Cheri){color} {color:#0000ff}DONE: ordered 1-14-08{color}
{color:#000000}ACTION:{color}&nbsp; confirm we have 3 swapable EM cables&nbsp; (Jim) {color:#0000ff}DONE: confer w/group and decide 1 spare is enough{color}

h3.


h3. MFB

Discussion Items:

•&nbsp;&nbsp;&nbsp; Syringe positioning

Syringe now oriented like other syringes on the core, i.e., pointing 'downward', and working well.&nbsp; Still waiting to test as several cables needed to be lengthened.

•&nbsp;&nbsp;&nbsp; Status of mixing column for extraction lysate.

Unable to build a 10cm mixing column because the use of 2 reducing unions requires a minimum of 50cm of tubing.&nbsp; Thus, mixing column is now 5x as long as it needs to be but waiting for Chris P. to do testing.&nbsp; Hope to test column next week around LLNL PCR visity.&nbsp;

ACTION:&nbsp; Jose to lengthen motor control cables (Addie).
ACTION:&nbsp; syringe motor mount.&nbsp; Mount 'upsidedown' for better lubrication.&nbsp; Changing motor for better gearing/speed ratio. (Addie)&nbsp; {color:#0000ff}DONE{color}
{color:#000000}ACTION:{color} confirm with email to Tony (Jim):&nbsp; {color:#0000ff}DONE{color}

h3. Software

Much discussion on how the code will be modified to accommodate a new thermal profile for puck heating.&nbsp; Brent suggested a very thorough plan of action, but was forced to accept a less elegant solution.&nbsp; Scott will provide nominal offsets and Brent will put in a mechanism to set gain/offset before every heating cycle.&nbsp; He has agreed to do this before the can cold-testing. (Brent)&nbsp;

Pressure tests; did four pressures.&nbsp; Chris P tried to grow lysate, but ran out of a reagent.&nbsp; We like 20-25psi---it's pumping like GG was. &nbsp; This number easy to change.&nbsp; He's made several parameters changeable.&nbsp; Chris P. knows most. &nbsp;&nbsp; Brent will create cheat-sheet for how these changes.

&nbsp;Firmware:&nbsp; servo-control works very well on MFB.&nbsp; Sampling at 64hz.&nbsp; this is different from all other dwarves so what should be do?&nbsp; Old code cannot change the divisor in the dwarves, but new Ruby can actually change the divisor, thus sampling at different rates.&nbsp; These are relatively large firmware modifications, so we will implement when the MFB goes in, NOT for Spring deployments.&nbsp;

Several small changes have resulted in a new firmware version that we +should+ update on Mack, Bruce, Neo.&nbsp; Brent will send email to everyone explaining changes.

+Action Items:+&nbsp;

ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent)
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)
ACTION:&nbsp; Update firmware on Mack, Bruce, Neo with the 'slightly modified version, and email the changes within this new firmware to everyone (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code (Brent):&nbsp; {color:#ff0000}Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress{color}
{color:#000000}ACTION:{color}&nbsp; Test pressure stuff (above); if problems, then heating stuff is dropped.&nbsp; {color:#0000ff}DONE (we believe 20-25psi delta will work like GG){color}
{color:#000000}ACTION{color}:&nbsp; Chris to give Brent water sample for running next week.&nbsp; Test running on bench at various pressures and run lysate test to test effects of different pressures (Chris/Brent) {color:#0000ff}DONE{color}

h3. Sphere and 4K DWSMS

Oil for DWSM has arrived and currenly being cold-tested.&nbsp; Doug met with local micro-pump rep, and is getting close to choosing the pumps he wants.&nbsp; All parts are ordered for the plastic model, which he will build in the Bldg B lab.&nbsp; He has the layout design and partial design for vavle actuators.&nbsp;

Nilo has inventoried all pucks and is receiving instruction on how to get them laser-etched.&nbsp; Will take first batch for etching next week.&nbsp; Following this [numbering scheme|ESPAPP:Puck Numbering System].
\\

{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
ACTION: Get quote for surface cans from Gene and place order (Jim):&nbsp; {color:#0000ff}DONE{color}
{color:#000000}ACTION{color}: discuss procurement and build schedule for next 2 cores (WHOI and CMORE funded) at 1-24-2008 mtg (in two weeks) {color:#ff0000}next meeting{color}.&nbsp;

h3. GUI Development

Kevin trying to have the Mission Script GUI in our hands before the [cold box testing.|2008 Q1-Q2 Schedule (rev 1)]\\
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h3. Minutes from Meeting to discuss ESP Phases, Protocol Runs, and Consumables
{section}
{column:width=60%}
We walked through the various assets and made a list of all instruments, phases, protocols, and consumables
# Instruments
## NEO
## GIGI
## Bruce
## Mack
# Phases and Protocols{note:title=Common Attributes}
All phases have flush intake, PHASE, then kill/end purge (can call out whether or not you want kill)
{note}
## HAB
### SH1
### lyfil
### SH2
### WCR
## DA
### DA1
### Dalyfil
### DA2
## BAC
### SH1
### lyfil
### SH2
### WCR
## invert
### SH1
### lyfil
### SH2
### WCR
## BACAR
### WCR
## QC
### WCR
## HABDA
### HAB phase
### DA phase
## Other protocols (can be skipped at times)
### Flush
### Kill/end purge
# Phase properties
## Max duration - all phases assume 1L sample, roughly 4 hours.&nbsp; HABDA would be about 6 hours.
# Protocol properties
## Duration
## Delay to sample
# Consumable Types
## Fix
## AqMeOH
## ab1
## ab2
## Lysis
## Diluent
## Sig1
## Sig2
## Sig3
## Con
## Sub 1
## Sub 2
## Wash
## CSR Flush (combine with CSV)
## CSV Flush
## PSR Flush
## Kill
## Waste1 (non-alcohol)
## Waste2 (alcohol)
## Power
# Bags/Containers/Storage:
## For NEO, how big are the capacities for the above consumables? (max volume is 2L)
# Protocol/Consumable Details (for each of the phase/protocol combination, what consumables do they use and how much?)
## Excel Spreadsheet?
# Mission Script Syntax (Work with Brent Roman)
{column}
{column:width=40%}
{panel:title=Attendees}
# Kevin Gomes
# Roman Marin
# Jim Birch
# Chris Preston
# Chris Scholin
{panel}
{panel:title=Agenda}
The focus of this meeting is to identify all the appropriate phases, protocol runs and consumables and their amounts (recipes) that will be available for planning a mission on an ESP instrument.
{panel}
{column}
{section}

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<property name="body"><![CDATA[h5. April 4, 2019

Just had 182 and 186 WCR pieces delivered.&nbsp; We will continue with the following numbering scheme:


{color:#000000}{*}TTT MYY-SSSS{*}{color}


{color:#000000}{*}Where:*{color}


{color:#000000}{*}TTT is the three-letter puck type: HV2, LAF, SAF, SH1, SHT, or WCR. Note that HV2 and SHT appear on tops only, and SH1 appear on bottoms only.*{color}


{color:#000000}{*}MYY is the month (M) and year (YY) in which the puck was manufactured. The month is represented by a number, 1 - 9 for January to September, or the letters, A, B, or C for October, November, and December, respectively. The year, YY, is represented by two numbers for the year.*{color}


{color:#000000}{*}SSSS is a four-digit serial number for the puck (0000 - 9999).*{color}


{color:#000000}{*}The following are examples of serial numbers:*{color}


{color:#000000}{*}SHT 410-1234 is a serial number for an SHT puck top that was manufactured in April, 2010 (410).*{color}
{color:#000000}{*}SH1 410-4321 is a serial number for a SH1 bottom that was manufactured in April, 2010.*{color}
{color:#000000}{*}WCR A10-1008 is a serial number for a WCR puck top or bottom that was manufactured in October, 2010 (A10).*{color}\\

h6. Our current (July, 2014) puck count is [here|^2014_PUCK _INVENTORYv2.xlsx|MBARI puck count].&nbsp;

Email from Scott, January 9, 2008 (updated 1-15-2008):

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note that we have yet to make a full batch of high-volume snap pucks, but when we do, those will be labeled 1HV (top and bottom).

Here is who is doing our etching:

LaserMark
2109 O'Toole Ave. Ste S
San Jose, CA 95131
Phone 408 433-9333
Fax 408 433-9343
\\
\\

Here is what I have packed up for etching:
| Type | Top/bottom | Numbered | Amount | NOTE |
| WCR | Top | 040-079 | 40 | \\ |
| \\ | Bottom | 040-079 | 40 | \\ |
| LAF | Top | 040-078 | 39 | 1=Missing |
| \\ | Bottom | 040-078 | 39 | 1=Missing |
| SAF | Top | 040-075 | 36 | 4sent to Gregg D |
| \\ | Bottom | 040-075 | 36 | 4sent to Gregg D |
| SHT | Top | 080-159 | 80 | \\ |
| SH1 | Bottom | 080-159 | 80 | \\ |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 390 | \\ |
\\
\\

I also sent 1 WCR puck (top&bottom) as a font sample.&nbsp; When these come back I will pack up the ones that are to be re-numbered(SHT2000-079).&nbsp; I haven't received a quote yet but Laser Mark said about $2 each piece + shipping.
\\

{color:#ff0000}UPDATE 3/24/08{color}

The SH1 tops that were misprinted are going to be sent out tomorrow to be re etched along with one of the LAF's that escaped detection last time:
| Type | Top/bottom | Numbered | Amount | NOTE |
| LAF | Top | 079 | 1 | Found the Lost 1\! |
| \\ | Bottom | 079 | 1 | \\ |
| SHT | Top | 000-079 | 80 | Old etching to be X'd out |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 82 | \\ |
That is all for now
\\
\\
\\

{color:#ff0000}UPDATE 2/24/09&nbsp; There have been several iterations of the above serialization process since this was last updated.{color}&nbsp;

Here is where we now stand:
| This   is an inventory of pucks that have been serialized and are available for   use.&nbsp; | \\ | \\ | \\ |
| There are   aprox. 1200 more pieces (or 600 more pucks) that have yet to be serialized. | \\ | \\ |
| They are   located in the 'B' building lab | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| Type | Top/Bottom | Lot 2 | Lot 2 | Lot 3 | Lot 3 | Lot 4 | Total | \\ |
| WCR | Top | 40 | 40 | 40 | 39 | 40 | 199 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 40 | 40 | 200 | \\ |
| LAF | Top | 40 | 40 | 40 | 38 | 40 | 198 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 36 | 40 | 196 | \\ |
| SAF | Top | 40 | 36 | 40 | 39 | 40 | 195 | \\ |
| \\ | Bottom | 40 | 36 | 40 | 40 | 40 | 196 | \\ |
| SHT | Top | 80 | 80 | 80 | 80 | 80 | 400 | \\ |
| SH1 \\ | Bottom | 80 | 80 | 80 | 77 | 80 | 397 | \\ |
| Total | \\ | 400 | 392 | 400 | 389 | 400 | 1981 | 990.5 |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | pieces | pucks |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| The   lot number refers to the 4th place in the serialization code:&nbsp; | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 letter type | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 1 digit lot number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 digit individual part number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| All parts   are numbered 000-079 ( except where some are missing) for each lot EXCEPT for : | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SHT=000-159 | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SH1=000-159 | \\ | \\ | \\ | \\ |
{color:#ff0000}{*}UPDATE August 11, 2010{*}{color}

&nbsp;Puck order from McLane arrived.

Rec'd&nbsp; 160 SH1, and 80 ea of LAF, SAF, WCR, HV (consists of HV top and SH1 bottom), all laser-etched.

PO 1010318
\\

Here is their email explaining their numbering system (sent Jan 14, 2010):
{Info:title=Mclane Numbering Scheme}
{Info}
From: Tim Shanahan \[mailto:tshanahan@mclanelabs.com\]
Sent: Thursday, January 14, 2010 8:52 AM
To: 'Birch, James'
Cc: 'Pargett, Douglas'; 'Jensen, Scott'; Everlove, Cheri; 'Scholin, Chris';
Yuki Honjo (yhonjo@mclanelabs.com); Ivory Engstrom
(iengstrom@mclanelabs.com); Mike Mathewson (mathewson@mclanelabs.com)
Subject: Puck serial number format

Hello All,

We've been thinking about the serial number format for the pucks and we'd
like to suggest some modifications.&nbsp; I'm concerned about duplicating lot
numbers and the potential for having runs bigger than 1000 units.

At least for now, I think there's the possibility of McLane and MBARI still
continuing to make puck independently.&nbsp; Keeping track of the current lot
number could be problematic.

So I propose the following:

TTTMYYSSSS

TTT for type code as below.

MYY for date code in
M= 1 - 9 for Jan - Sept, A B or C for Oct Nov & Dec

YY for 2 digit year

SSSS for serial number 0000 - 9999

Also, this ensures that there never a letter I or O.

This increases the total number of characters from 7 to 10.
{info}
{info}
&nbsp;
\\
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Absent: Kevin, Wayne, Chris S.&nbsp;

h3. Instrument Builds/Tech Transfer

* South Carolina person here {color:#ff0000}August 21-29{color} to run Mack & Bruce (Tina Mukulsky (sp?))
* Bruce temp calibrations finished and verified.&nbsp; Mack will be finished by the end of today.
* Roman will help with verification check.
* Wiring harnesses for CMORE/NSF/Moe are in and being QC'd.&nbsp; Will wait to order MFB harnesses when grill layout is finalized.
* Gripper board and puck sensor boards have very slight redesigns.&nbsp; Still waiting to determine how many of each to make, and whether we should switch out current machines with new redesigned boards.

h3. MFB

* motors on grill working, but encoders not.&nbsp; (FRIDAY update:&nbsp; encoders now working)
* We must come up with naming convention of the MFB's for accessing via software.
* Will daisy-chain power from SPE to PCR module.
* Serial connection from PCR to either host card or a laptop.
* Much discussion of whether to include a host card on each MFB.&nbsp; Without the card, stand-alone MFB's will require laptop to run; they would be unaffected when attached to the core.&nbsp; While it may impact low-level software development to have a host-card on each MFB, the simplicity of a _complete_ stand-alone unit for the external user dictates mounting a host card.
* We must build several Power Boards; will populate here at MBARI (Scott)
* Closed-cell foam being explored for insulating the SPE block

h3. Software

* Brent has 2 radios working simultaneously; working on adding a third.
* Second in priority is the limit-switch testing, a critical path item for DWSM
* At LINUX expo, Brent talked to people about putting WiFi on mooring, good for 7-8 miles los.&nbsp; We should explore; perhaps contingency project in 2009 for Brent.
* Antenna lease agreement finished and out for comment.&nbsp; We will need to purchase serial cable to connect house to radio.

h3. DWSM

* Sphere update--We have had conference call to Tapemation.&nbsp; They expect to get spheres on lathe in 4 weeks, completed by end of October.&nbsp; Mark Brown looking into pressure testing facilities.
* Doug has found affordable Ti screws.&nbsp; Will use 6-40's and tap sphere accordingly.&nbsp; Tapemation has been notified.
* No word yet from El Camino.&nbsp; Doug predicts 3 weeks for bell housings.
* Many parts sent to machine shop. Mark B told that DWSM stuff is top priority. 'Soup Can' probably sent to Tapemation.
* Most COTS parts are here--still need Mini-Con's, Swageloc, various connectors/cables
* Electronics--Boards laid out;&nbsp; Scotts&nbsp; miniEE review probably the week of Aug 18
* Doug to have informal discussion with DMO about weight balance issues related to the as-yet-to-be-designed elevator.&nbsp;

h3. Other Items

* syringes.&nbsp; Scott has the new 1ml and 2.5ml but the 25ml leaked and were sent back.&nbsp; Klone had a plan for fixing , but that was 6 weeks ago.&nbsp; Scott will contact...
* 11000 D-cells; account # provided and order has been sent to Jose.
* Decision is to go with plastic radio boxes, but with larger tapped holes with no metal inserts.&nbsp; Scott will talk to Jose about their manufacture.]]></property>
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h3. Instrument Builds

* South Carolina person here {color:#ff0000}August 20-29{color} to run Mack & Bruce (Tina Mukulsky (sp?))
* &nbsp;Temp re-calibrations of Mack finished and has updated firmware
* Bruce has 2 of 3 calibrations; will be finished by end of the day
* Roman will help with verification check.
* Scott will spearhead effort to get 3 new radio boxes built

UPDATE:&nbsp; Friday, a combination of issues caused puck-temp sensors to be torn from their mounts, so machines will be recalibrated beginning Monday.
* Mooring update:
** Scholfield is leading the charge on building the 3rd mooring
** We need to order 1100 D-cell alkalines.&nbsp; Scott needs charge number&nbsp;

h3. MFB

* cables are finished
* software integration moving along nicely
* grill is very close to being operational.&nbsp; Still waiting on SPE heater from Mike and the LLNL PCR block.
* Need Scott to integrate SPE heater onto the heater board
* We should think of insulating the SPE block

h3. DWSM

* Sphere update--point cloud has been provided by Tapemation
** issue is how to cut
* Ti screws might be very expensive for the size we want.&nbsp; Doug exploring helicoils as good alternative.&nbsp; Decision needs to be made before Tapemation begins machining.
* Bell Housing needed slight modification since part ordered by El Camino was too short.&nbsp; Other parts are now in machine shopl
* Doug wants to try and do swiss cheese plate in-house.
* Most COTS parts are here--still need Mini-Con's, Swageloc, various connectors/cables
* Electronics--Boards laid out;&nbsp; Scott wants miniEE review late next week
* Note about elevator assembly-\- want to be able to open and 'get at' sphere
* &nbsp;
* &nbsp;

h3. Other Items

* Kevin estimates $10K for machine-state visualization software
* Brent wants to test limit switches--can do w/ stuff on his desk
* Still must do radio test--configuration with 3 radios
* Brent found another antenna place
** we will draw up a 'contract' detaling time, it's our stuff, we'd pay for his cable, give notice of renewal--Jim to work with Brent on this.]]></property>
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<property name="body"><![CDATA[Doug on vacation July 14-July 28.

present: Jim, Brent, Scott, Addie, Chris S., Wayne
absent: Doug, Cheri&nbsp;

h3. Instrument Builds

* South Carolina person here {color:#ff0000}August 20-29{color} to run Mack & Bruce.
* &nbsp;Brent has found that the front and back puck sensors respond differently&nbsp; to changes in ambient temp (front 19-26%; back 30% of ambient).&nbsp; Thus we should recalibrate to the front sensor, a change that should be transparent to the user.
* 11:00am Monday (7-28).&nbsp; Brent, Addie, Cheri, Wayne meeting to discuss integrating MFB with NEO
* Scott will spearhead effort to get 3 new radio boxes built

h3. MFB

* all pieces from shop should be here by today (except SPE block)
* Jose working on wiring harness
* Must makesure tombstone works with latest Ruby code, then can begin integration.&nbsp; Addie/Brent will work on this separate from above meeting.

h3. Software

* DWSM software is very close to being ready to test
* TUESDAY--Brent/Scott/Wayne are going to pick a part, and populate rev.1 dwarves to test wether 2nd gen of I2C buses are less 'funky' than gen 1.
* WED.--Gomes/Schramm/Roman/Scholin/Birch meeting to discuss GUI needs next year.&nbsp; For discussion:&nbsp; machine state, mission scripting, data parsing.
* Wayne having great difficulty pulling base C code in order to use new compiler.&nbsp; Much work to reduce errors, but he will continue looking into depth of problem.
* Brent waiting to hear from our potential antenna candidate site; if no word by next Thursday, we move to a yet-to-be-determined plan B.

h3. Other Items

* Of all issues on Brent's 'to-do' list after last deployment, only three remain:
** why did radio link quality decrease?
** did RS232 CTS handshake line to radio modem fail?
** failed email messages are not queued for later retransmission.]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 10, 2008*

*10:30am-12*
Present:&nbsp; Jim, Chris S., Brent, Doug, Kevin G, Cheri, Addie, Scott

h4. *After today meetings will be 11-12am*&nbsp;


h3. Tech Transfer

Action Items from last week:

ACTION: Brent will show Cheri and Addie how to read log (Brent & Cheri & Addie)&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; run a sample on GG to compare pressures to NEO (Scott)&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}
ACTION: check with Jose and Tom about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose still diggin through BOM to figure out what we can order&nbsp; (1/4 way through)
ACTION: discuss test box design with Jim Scholfield (Cheri)&nbsp; {color:#0000ff}DONE:{color} Jim and Cheri and Scott discussed design; he's ordering parts.&nbsp; Maybe end of next.
ACTION:&nbsp; move connectors from 1K to the test box (Doug & Cheri)&nbsp; {color:#0000ff}DONE{color}: Been pulled off 1K and now at Jim S (electrical).&nbsp; Fluidic connectors--we are going to use ones that Mike made.&nbsp; Doug thinks they are in lab downstairs.
ACTION: Clean B125 lab for CMORE visit (everyone)

Discussion Items:
•&nbsp;&nbsp;&nbsp; Surface can quote from IMT:&nbsp; 3 cans = \~$37K

{color:#ff0000}ACTION{color}:&nbsp; cannot purchase on 708 grant yet.&nbsp; 701312.04 should take all cost.&nbsp; Change:&nbsp; Order only 2 cans (Jim)

•&nbsp;&nbsp;&nbsp; Mooring supplies for network deployment

No one knows everything.&nbsp; We can get by with 2, but we really need 3.&nbsp; Doug says it's 6 months of Jim S. time, but Chris thought 1 month.&nbsp; Discussion ensued on what was necessary and we agreed that we could get by with our two complete moorings with appropriate spare parts.

{color:#ff0000}ACTION{color}:&nbsp; confirm we have 3 swapable EM cables and purchase spares from 701312.04 (including labor) (Jim?)

•&nbsp;&nbsp;&nbsp; Update on test chamber and test chamber fixtures

•&nbsp;&nbsp;&nbsp; Arm status (see above)

Failure last week was due to an assembly issue on arm that caused binding.&nbsp; Reassembly found broken wires in home sensor.&nbsp; Friday was working great at 10 degrees all weekend.&nbsp; Checked Monday morning it looked fine.&nbsp; Lowered temp to 2C and Tuesday found ribbon cable home sensor cable was broken.&nbsp; There is a loop for a strain relief.&nbsp; Brent suggests mylar cable used in printer.&nbsp; Chris suggests a 'ticker' to count cycles so we know when things should be changed.&nbsp; Revalving has started on Mack; 7 of 8 have been done.&nbsp; Modifying mount on 8th one.&nbsp; Should be done by Monday.

We will use 'non-ideal' arms for Spring deployment, but when we order new hands, we will order the correct 4-bar holes.&nbsp;

{color:#ff0000}ACTION{color}:&nbsp; talk to Jose to figure a solution to broken home sensor cable. (Scott/Doug/Cheri)

{color:#ff0000}ACTION{color}: Contact MAXON about forearm motors (Cheri)&nbsp;

h3. MFB

ACTION:&nbsp; Order custom valve heads (Addie)&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; syringe motor mount.&nbsp; Mount 'upsidedown' for better lubrication.&nbsp; Changing motor for better gearing/speed ratio. (Addie)&nbsp; {color:#ff0000}SEE BELOW{color}
ACTION:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (Scott/Brent/Addie):&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; Sleepy board given to Brent, w/ Addie using a dwarf board (Addie):&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; talk to Tony and get timeline on next MFB (Jim):&nbsp; {color:#0000ff}DONE{color}

Discussion Items:
•&nbsp;&nbsp;&nbsp; LLNL schedule---Tony coming Jan. 23.&nbsp; DONE

{color:#ff0000}ACTION{color}: confirm with email to Tony (Jim)

•&nbsp;&nbsp;&nbsp; Syringe lubrication

Syringe motor has been changed to one with higher encoder count.&nbsp; Should be no problem to get slower speed; pin numbers were different (10 new vs 6 old).&nbsp; Brent and Addie working on calibrating it.&nbsp; Config file is now cleaned and only contains MFB stuff.&nbsp; Flipping syringe will allow lube to sit on top of plunger.&nbsp; Syringe will be flipped.

•&nbsp;&nbsp;&nbsp; Mixing column for extraction lysate.&nbsp; Discuss construction.

Cannot put PEEK 2ml ID tubing into our smaller fittings.&nbsp; But can use 1/4-28 fitting normally.&nbsp; So Addie instructed to build simply stand-pipe structure with PEEK.&nbsp; May look at Optimize.com who make HPLC mixing chambers to see if they have these chambers. Addie going to check out standpipe design/structure.

h3. Software

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; change laptops and ARM boards and install the new Ruby interpreter (Brent):&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code (Brent):&nbsp; {color:#ff0000}Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress:{color} Wayne still on vacation

Discussion Items:
•&nbsp;&nbsp;&nbsp; Sampling technique.&nbsp; Greater pressure or 'pulsing' or both?

Brent has maxed the vacuum in the syringe without cavitation but unknown if this is how 'natural' water works.&nbsp; Chris can provide natural sample.&nbsp; To get more sample volume do we want to experiment with a greater deltaP?&nbsp;

{color:#ff0000}ACTION{color}:&nbsp; Chris to give Brent water sample for running next week.&nbsp; Test running on bench at various pressures and run lysate test to test effects of different pressures (Chris/Brent)&nbsp;

•&nbsp;&nbsp;&nbsp; Themal control hardware.&nbsp; Necessitate a firmware change?

Scott has a new sensor setup.&nbsp; Goal would be to eliminate funny ramps in RUBY to avoid overshooting.&nbsp; These controls are already in the DC motor controllers, so should we use this control in the temp control?&nbsp; Worry is it's a big change.&nbsp; Firmware/Ruby must both change.&nbsp; This started because we don't always 'get' to our required temperature; its a function of ambient in the can.&nbsp; Chris; if offset is pretty well known, then we could live with it, if offset is big, it could screw up our array results.&nbsp; We can change the hardware, but getting software changed over may take too long.

{color:#ff0000}ACTION{color}:&nbsp; Will change the hardware, and look at offsets (Scott)

This will dictate next step.&nbsp;

•&nbsp;&nbsp;&nbsp; Modification of friction compensation w/in servo code.

In progress, but not as important as heating offsets.

•&nbsp;&nbsp;&nbsp; Other software changes and test plan for their implementation

{color:#ff0000}ACTION{color}:&nbsp; Test pressure stuff (above); if problems, then heating stuff is dropped&nbsp;

h3. Sphere and 4K DWSMS

ACTION:&nbsp; Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott).&nbsp; {color:#ff0000}In progress{color}.

Get Nilo to take lead on this with Roman oversight.

ACTION: will try and have model done by end of Jan--depends on pumps (Doug) {color:#ff0000}In progress{color}

Can readily put together plastic housing.&nbsp; Still working on type of pumps

ACTION: Get quote for surface cans from Gene and place order (Jim):&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price

Discussion Items:

•&nbsp;&nbsp;&nbsp; Serial numbering of old pucks
put this on Confluence

•&nbsp;&nbsp;&nbsp; Status of new puck order
One set (carousel) by March 3; we need to tell them when we need the next set.

•&nbsp;&nbsp;&nbsp; Order and manufacture of screens, frits, polysulfone
photofab gave too large holes so too weak.&nbsp; Laser cut would be more accurate.&nbsp; Give them (photofab) hard spec with feedback.&nbsp; Chris has info on the scintered frits and ordering specs.

{color:#ff0000}ACTION{color}:&nbsp; get inventory from Roman (Jim/Roman): laser-etch pore size for scintered frits


•&nbsp;&nbsp;&nbsp; Pressure pots ordered? Yes
•&nbsp;&nbsp;&nbsp; Status of 4K sphere:&nbsp; 2-piece pattern pictures sent to us: shipping them over to casting house

•&nbsp;&nbsp;&nbsp; Procurement schedule for next 2 cores

We don't have money from WHOI until late 2008.&nbsp; CMORE we're in the middle of that year

{color:#ff0000}ACTION{color}: discuss build schedule for next 2 cores at 1-24-2008 mtg (in two weeks).&nbsp;

h3. GUI Development

&nbsp;Kevin updated on GUI development.&nbsp; He would like to use his GUI tool to generate a mission-script for the Feb cold-room test.&nbsp; He needs reagent volumes to get accurate usage display.&nbsp; We will want to generate mission script the last week in January.&nbsp; Will meet tomorrow (Jan 11) to discuss volumes with him.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 7, 2008*

*11am-12*
Present: Jim, Doug, Scott, Brent, Cheri, Chris S., Kevin

Absent: Addie&nbsp;

LATEST Deployment Schedule is [HERE|ESPAPP:2008 Q1-Q2 Schedule (rev 3)].&nbsp;

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.
** {color:#339999}Brent wants to re-do some temperature calibrations with core placed inside box to remove air current effects.&nbsp; Will calibrate thermocouples this PM and get collection-side offsets tomorrow so science can start using on Monday the 11th.{color}
** {color:#339999}This PM Cheri will also calibrate Mack's hand{color}

* &nbsp; Mike Parker Machining list \-\- working quickly through it
** {color:#339999}Doug/Cheri worked on prototype of an adjustable temp sensor and will talk to Mike about it.&nbsp; Needs a priority.&nbsp; Will implement into Bruce, Mack will remain as is.{color}

* New syringes.
** {color:#339999}Still not heard back from company{color}

* Screens and scintered frits
** {color:#339999}Yesterday Scott sent plans to company for quote.{color}
** {color:#339999}We will order enough screens for 6 instruments.&nbsp; As soon as we have screen costs, we'll know how much money we have left and order scintered frits accordingly{color}

* Camera Discussion
** {color:#339999}Chris S. has found the 2x2 binning works well, so cameras will remain at f2.5 with \~2mm focus depth-of-field.{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

h3. MFB

Discussion Items:

ACTION:&nbsp; Addie to look at heating profile times to make sure we are not cooking our reaction. (Addie)&nbsp; {color:#ff0000}In progress{color}

h3. Software

* puck heating control
** {color:#339999}Brent needs one more day to get a better approximation on the collection side.&nbsp; Needs another puck--should be finished today.{color}
* Brent added code that reversed polarity of the motor encoders, since these new motor-mounts have encoder rotating opposite direction of originals.

+Action Items:+&nbsp;

ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment (Brent): {color:#ff0000}Low priority Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carousal and alignment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}

h3. Sphere and 4K DWSMS

* Sphere update
** {color:#339999}Wah Chang has changed their procedure, and will only make one part, have it checked, then cast the second article.&nbsp; If something wrong with the first one, we will be 2 months late and must reschedule all the late 2008 deployments.&nbsp; If all goes well, 2nd half will be cast in June.&nbsp; Can get both from Tapemation in August.&nbsp; Send to Port Hueneme for pressure testing and get back mid-Sept.{color}&nbsp;

* DWSM progress?
** {color:#339999}Aqualung up a running.&nbsp; It does everything except accurately measure volumes pumped.&nbsp; Finding correct pumps has been difficult.&nbsp; Doug has several backup ideas including going to a syringe/piston system.&nbsp; Stirring pump found to generate much heat when submerged in oil, as well as leach out lubricant/coating so several ideas floated to balance friction (and thus power consumption) and stirring capability.&nbsp; Maybe try lighter oil.{color}
* Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}

{color:#000000}ACTION:{color}&nbsp; Waiting for company to return yes/no on whether they can manufacture screens to mass instead of size. (Doug/Scott)&nbsp; {color:#0000ff}Finished{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price.&nbsp; Must order BATTERIES for deployment.
ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)&nbsp;

h3. GUI Development

* Mission script GUI introduction

Kevin to meet with Brent to discuss mission script GUI.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
\\
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<property name="body"><![CDATA[h2. Outline of instrument plan for Jan-Jun, 2008

Mack has been cold tested with new hand and new valves and Roman Flush run to check tubing.

Temp calibration Jan 29-Feb 5.

Science gets MACK Feb 6 and will prep reagents, generate mission script, run sub-protocol tests&nbsp;
# One month cold test of Mack w/ his new valves/hand starting Feb 14.
## OBJECTIVE:&nbsp; get through a full carousel of pucks
## test should last most of 4 weeks (although 3 weeks would be acceptable)
# March 6 is earliest we pull and deem a success.&nbsp; Once pulled, we replace with Bruce for box test.&nbsp;
# Prep for Spring deployments (Mar 14 \-->Mar 19)
# {color:#ff0000}{*}Deploy{*}{color} MACK (March 20-Shana Rae)
## {color:#0000ff}{*}Recover{*}{color} MACK Apr 10, {color:#ff0000}{*}Deploy{*}{color} BRUCE \-\- Shana Rae
# &nbsp;{color:#0000ff}{*}Recover{*}{color} BRUCE, {color:#ff0000}{*}Deploy{*}{color} MACK (May 1 \-\- Zephyr)
# {color:#0000ff}{*}Recover{*}{color} BRUCE (May 27), {color:#ff0000}{*}Deploy{*}{color} *both* MACK and NEO (May 28 \-\- Zephyr)
# End mission Jun 30.
\\
\\
\\
\\

(Revised 31 Jan 2008) ]]></property>
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<property name="body"><![CDATA[Priority, What we need, (number).&nbsp;

Black \--> we do in house, {color:#0000ff}Blue \--> can be sent out (Mike decides){color}
* -1, Mushroom caps - 1003526-004 \-(20)- {color:#ff0000}-\- Mike has made (5) and will send the rest out for quote (1/31/08)-{color} {color:#000000}\- Rcvd 3/3/08{color}
* -1, Bulkhead V. mounting brackets - P-200325-07 - (6)- {color:#ff0000}(02/04/08){color}{-}1-Mike,- {color:#0000ff}{-}Waste container supports - 1003526-003 - (6)-{color} {color:#ff0000}-\- Mike has sent prints out for bid (1/31/08) PO #0810307{-}{color} {color:#ff0000}\-{color} {color:#000000}Rcvd 3/3/08{color}
* -1-Mike,- {color:#0000ff}{-}Bag Hanger Assemblies - 1003523-01-02-03 - (5)-{color} {color:#ff0000}-\- Mike has sent prints out for bid (1/31/08) PO #0810307{-}{color} {color:#ff0000}\-{color} {color:#000000}Rcvd 3/3/08{color}

| {color:#009900}Bag Assembly Parts&nbsp;{color} | {color:#009900}For 5 Instruments{color} | {color:#009900}We currently have{color} | {color:#009900}We thus need (minimum){color} |
| -Hoops- | 10L&nbsp; 5mL&nbsp; 15sm \\ | 4L&nbsp; 1mL&nbsp; 2sm \\ | -6L&nbsp; 4mL&nbsp; 13sm- {color:#ff0000}(02/11/08){color} \\ |
| Crescent Closet Bar \\ | 7 | 3 | 4 {color:#ff0000}Rcvd 3/3/08{color} |
| Bushing Assemb 4/instrument \\ | 20 | 14 | -6- {color:#ff0000}None Needed{color} |
* 2, Modem Battery cylinder - 10020051-01 - (1)
* -2,- {color:#0000ff}{-}Sample ports - 1002516 - (4)-{color} {color:#ff0000}(2/19/08){color}
* 2, spin can zinc down (3)
* 2, can-side CTD bracket (2)
* 2, {color:#0000ff}sample intake copper screen holder - 1002516-02 - (4){color}
* 2, bail locking plates (4)
* 2, adaptor plate for mooring (2)
* {color:#ff0000}2, Shaft Adapter for Maxon-to-Valve - Replacement for ShaftLoks \-&nbsp;(qty. 30?) -{color} {color:#000000}Provided Aluminum qty. 8. Still need ?{color}
* -3, CTV mount - 1002330-019 - (3)- {color:#ff0000}(2/04/08){color}
* -3, forearm motor shaft adaptor - 1002451-006 - (2)- {color:#ff0000}(02/05/08){color}
* -3, finger motor shaft adaptor - 1002451-006 short - (2)- {color:#ff0000}(02/05/08){color}
* -3, slot the encoder shafts (8)- {color:#ff0000}(02/11/08){color}
* {color:#ff0000}3 Parker Pucker Un-Stuckers - Solids and Prints ready (02/12/08){color}\\]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 31, 2008*

*11am-12*
Present: Jim, Chris S., Kevin, Doug, Cheri, Brent, Scott, Addie
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp;&nbsp;
** {color:#339999}Mack has been cold-tested and Brent is working on temp sensor testing.{color}
** {color:#339999}Bruce--all valves are in, hand mostly assembled, still to finish plumbing{color}
* Mike Parker Machining [list|Machinist build schedule (Feb 2008)] \-\- working quickly through it
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; {color:#339999}N{color}
** {color:#339999}New hands to be ordered this summer.&nbsp; XX hand assemblies + 3 sets of fingers with new fulcrum positions to replace the existing 'new' fingers{color}
* New syringe cost.&nbsp;
** {color:#339999}Still not heard back from company{color}
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp;
** {color:#339999}Jose still forming the database.&nbsp; Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612,&nbsp; maybe a subaccount (.99 for CIP)).{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp; {color:#0000ff}Finished{color}
ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp; {color:#0000ff}Finished{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#0000ff}Finished{color}

h3. MFB

Discussion Items:
* Getting excellent yields out of solid-phase-extraction--Good job Addie and Chris P\!\!
* Mixing column basically finished
* next week will make extract from seawater lysate and compare to bench-top
* in parallel, do dye tests with heater block.

ACTION:&nbsp; Hook up heater block and test diodes for fluorescence sensitivity. (Addie)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will work on figuring cable problem to three-way valves. (Addie) {color:#0000ff}Finished{color}
ACTION: Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie) {color:#0000ff}Finished{color}
ACTION: Fan not working on PCR module and Addie will try and track down why (check in various terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie); {color:#0000ff}Finished{color}

h3. Software

* puck heating control
** now can send a temperature to puck and it gets there in 2-3 minutes with little overshoot
* Brent would like to pull calibration values out into a structure, since they are different on each instrument

+Action Items:+&nbsp;

ACTION:&nbsp; Finish by Feb 6 the temperature calibration model, incorporating Scott's prior work if possible. (Brent)
ACTION:&nbsp; make another temperature puck (Scott)
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment (Brent): {color:#ff0000}Low priority Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}

h3. Sphere and 4K DWSMS

* Screen drawings.&nbsp;

Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}
* DWSM progress?&nbsp;&nbsp; {color:#339999}Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.{color}

{color:#000000}ACTION:{color}&nbsp; Waiting for company to return yes/no on whether they can manufacture screens to mass instead of size. (Doug/Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim): {color:#0000ff}Finished{color} (Tapemation is it unless we want to go back east)&nbsp;

h3. &nbsp;


h3. GUI Development

* Mission script GUI introduction

Kevin showed how to use the mission script GUI located [here|http://predator.shore.mbari.org/esp_gui/launch.jnlp].
Bugs for this GUI can be reported [here|http://oceana.shore.mbari.org:8082].&nbsp;
\\
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 24, 2008*

*11am-12*
Present: Jim, Doug, Scott, Addie, Kevin, Brent, Chris S.
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp; {color:#339999}Hasn't shuffled pucks yet.&nbsp; Almost finished testing{color}
* Update on valve cold-testing of MACK.&nbsp; {color:#339999}Still to begin{color}
* Jan 15-29 both Bruce & Neo to be re-valved.&nbsp; Progress? {color:#ff0000}Not begun{color} yet
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; {color:#339999}Not ready until cold-testing finished{color}
* New syringe cost.&nbsp; Acct to charge?&nbsp;&nbsp; {color:#339999}50 syringes&nbsp; \~$10K charge to 900612.&nbsp; May start to identify people that want these new syringes (Chris S.){color}
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp; {color:#339999}Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612 (look to see if he has time (Jim)&nbsp; maybe a subaccount (.99 for CIP)).{color}
* Mock deployment schedule and Spring field trials
* PROCUREMENT AND BUILD SCHEDULE FOR NEXT 2 CORES (WHOI & CMORE)

&nbsp;*Two Options for build of two more cores:*

Buy parts under another grant and then transfer charges to WHOI grant when money comes in in August 2008.&nbsp; This is dangerous as WHOI may not get money and if we've bought ahead, we'd be stuck with parts, and have hit another grant very hard.
CMORE machine will initially be stationed here at MBARI but eventually goes to CMORE partner.&nbsp; The best plan is to use BRUCE/MACK as the WHOI & CMORE machines, and have parts for their replacements on hand. &nbsp;&nbsp;

Chris thinks--do we know what we need to order.&nbsp; Get all ready to cut and look to mid-summer for procurement and build starting in Sept.&nbsp; By that time more money comes through and we could add to the purchases.&nbsp; This applies to all Jose's boards except the MFB boards.&nbsp; Now we should order enough dwarfs for MFB and spares. For MFB boards split between 701312 and 800560.&nbsp; Make sure subaccount charges are correct.&nbsp; The summer order would be the rest and the long-lead orders.&nbsp;
\\

Second MFB is parted and here.&nbsp; Chris and Jim will work with grants to make sure money is spent correctly (reallocate MOORE monies).

Neo has been capitalized so buying any more parts goes to a different account (maintenance or equipment supplies, not the NEO CIP account).&nbsp;

[Q1-Q2 2008|2008 Q1-Q2 Schedule (rev 1)] schedule has slipped.&nbsp; Must shift our schedule back one month.&nbsp; Maybe can shave mock-deployment by running harder/faster.&nbsp;

ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp;
\\

+Action Items+

ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp; {color:#ff0000}In progress:{color}

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}

h3.


h3. MFB

Discussion Items:
* Motor control cables lengthened?&nbsp; {color:#0000ff}Finished{color}

problem in cable that goes to 3-way valve.&nbsp; Jose can't figure it out.&nbsp;

ACTION: Will work on figuring cable problem. (Addie)
* Heater block re-plumbed?&nbsp; Owner's manual written detailing new drivers?
* Begin PCR tests?.

LLNL commands are now in Ruby (via Bob Herlien) and Addie has placed on Confluence a '[users manual|ESPAPP:Micro-Fluidics Block^~$B PCR Module Users Manual V1.0.doc]' for the PCR module.&nbsp; Software works well and easy to write scripts.

Fan not working on PCR module and Addie will try and track down why (check in various terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie)

ACTION: write Tony at LLNL for advice. {color:#0000ff}FINISHED{color}&nbsp;

Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie)&nbsp;

h3. Software

* Gain/offset for heating cycles installed?&nbsp; Still trying to test
* Has 'Cheat Sheet' for new sample collection parameters been distributed? (Not done)
* Firmware updated on Mack, Bruck & Neo? still testing

+Action Items:+&nbsp;
ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent): implemented but figuring when it should happen.&nbsp;
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)
ACTION:&nbsp; Update firmware on Mack, Bruce, Neo with the 'slightly modified version, and email the changes within this new firmware to everyone (Brent) DONE

Brent will work on operational model for temp control.&nbsp; Get it ready for Sept that will be implemented with the MFB. (Brent)&nbsp;

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress{color}

h3. Sphere and 4K DWSMS

* Oil cold testing.&nbsp; Finished?&nbsp; {color:#339999}100 cst goes 150 cst when in cold.&nbsp; It's a significant increase but can be counterd by buying lower viscosity oil.{color}
* &nbsp;
* Screen drawings.&nbsp; Checked?&nbsp; Ready for order?&nbsp; Photofab drawings have been looked at and they have a new spec to send to PFI.&nbsp; The way they fabbed last time they took out too much b/w holes.&nbsp; Doug wants them etched to a certain mass.&nbsp;

ACTION:&nbsp; Scott to send samples and current idea to see if they can do it to weight. (Scott will mail samples to them)&nbsp; Chris and Roman have spec for scintered frits and are discussing how many to order.&nbsp; They have a quote.

* Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}
* DWSM progress?&nbsp;&nbsp; {color:#339999}Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.{color}

No word on sphere.&nbsp; Discussion about Tapemation machining and how we should get insurance or discuss protection.&nbsp;

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim)

{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
&nbsp;

h3. GUI Development

* Mission script progress

ACTION:&nbsp; Will try and have mission script GUI out next week.&nbsp; Kevin will meet with Chris S. (Kevin)
* Adjustment of project #'s in JIRA

ACTION: Kevin will delete one account and the one to use is ESP Gen II. {color:#0000ff}FINISHED{color}\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. ESP Meeting


h4. &nbsp;Items:

* &nbsp;Chris P, Roman, Mike P meeting at 2:00pm today to finalize the BOM for the MFB
* Most people could make a March 14 field trip to Sandia in Livermore.&nbsp; Will check with Ken Patel to see if it works for them.
* Jim will get Material Transfer Agreement for the Qiagen material;&nbsp; Scott Burrows may come visit March 6.
* We need to set up Confluence page to allow LRAUV access
* {color:#cc0000}Will come up with decision tree on technologies to use by Feb 28.&nbsp; Will then Review on March 1 when Chris can attend.{color}

h4. Puget Sound Deployment

* &nbsp;2 deployments, both using cell-phone and on piers.
** First will be late May to late June, while Vera is teaching a class at Friday Harbor.
** Second will be in August in Samish Bay (lat/long is 48.610416,-122.437445).
** NOAA has no operating funds and will need arrays, pucks, and reagents.
** deployment logistics still to be worked out.
** We will want to install HOBO's in their machine to watch for temp fluctuations
** {color:#cc0000}Must set-up site-visit dates.{color}

h4. Cawthron

* Chris and Kevan have a reagent list.&nbsp; Roman to provide what Puget Sound will need.&nbsp; This order and the dates needed will be given to Spyglass this week(?)
* &nbsp;Look into bonding our container shipment to speed through customs.

h4. 3G ESP

* &nbsp;Spoke at length with Doucette/Connel about their reagent needs in the Gen 3 instrument.&nbsp; Bead beating looks like a great thing for them.
* Right now, aqueous methanol extraction works and would require 3 reagents total:&nbsp; aq MeOH, primary Ab, PNA buffer.
* from 1 ml of aq MeOH lysate, pull 250ul for Ab labeling and/or 250ul for PNA labeling before sending to SPR.
* Work on Dissolved DA revolves around running filtered water through a resin to concentrate.&nbsp; Hope is that methanol would be the eluate and everything downstream would be same as above.&nbsp; form factor of resin column is not decided yet.&nbsp; Greg and Nick working on this right now.]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Mar 6, 2008*

*10:00 am* Present: Pargett, Jensen, Marin, Everlove.

h3. Tech Transfer


h6. Discussion Items:

Mock fridge mission, 3/12 to 3/19

Loading and QC of reagents on Monday. Puck loading on Monday.&nbsp;Mack going into the fridge on Tuesday.

Still need ISUS, have CTD, need to be batteried and programmed.

Scott will test GPS tracking outside, won't be active during mock mission.

Mike will make more valve drive bushings out of alumingum.
\\

h3. MFB

Not discussed.

h3. Software

Not discussed

h3. Sphere and 4K DWSMS

Torque testing shows we can get the LVLP pump on a dwarf, the HVLP will be marginal, and the LVHP will need a seperate amop. Scott is working on that arrangment.

h3. GUI Development

Not discussed]]></property>
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<property name="body"><![CDATA[[HAB-DA Process Diagram|^G3HABDA-0.1.pptx]Ver 0.1
[HAB-DA Cartridge written protocol|^3G_HABDA_Ver0.1.doc]Ver 0.1

[Sequential Chemistry Filter Module|^G3SeqChem-0.1.pptx]Ver 0.1


\\  [^G3 Modular Cartridge 05-02-12.pptx] Revised: May 2, 2012]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 28, 2008*

*11am-12*
Present: Doug, Chris S, Scott, Addie, Brian, Cheri

h3. Tech Transfer


h6. Discussion Items:

* Update on Mack: Mack is beautiful. Doing it's first full phase, right now.
* Mike Parker contacted about piezoprinter problems (holding down membrane, cutting out disks) and is designing solutions.&nbsp; Also will be approached about a puck holder.
* Puck Etching: Next batch to go out... 701312.06 Puck CIP.
* New syringes: Scott to check on them.
* Screens and scintered frits: Leter coded frits were ordered by Jim.
* Need to define a mission script next week&nbsp;for cold test.

h3. MFB

* Weak pos on Mon, but nothing since. Found that reagents were dead. New reagents on the block now.
* LLNL replacing components on the new boards.
* April fecal water sample purification test.

h3. Software

Not discussed, Brent on vacation.

h3. Sphere and 4K DWSMS

* Sphere update
** {color:#000000}No word or update from Wah Chang.{color}

* {color:#000000}DWSM progress?{color}
** {color:#000000}Revisiting motor for pumps. Sampling condition would be very power inefficient. Should have a power budget and motor/pump nailed down in a week.{color}
** Doing torque testing of pump since most of power is lost in running friction for the LP pumps.
* {color:#000000}Battery boxes?&nbsp; IN{color}
* {color:#000000}Batteries oredered? Yes{color}

ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)
ACTION:&nbsp; New surface can lid discrepency, Jim was going to meet with Gene about it. (Jim)

h3. GUI Development

Brian had image handling questions...]]></property>
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<property name="body"><![CDATA[h3. Outline of instrument plan for Jan-Jun, 2008

Mack has been cold tested with new hand and new valves and Roman Flush run to check tubing.

Science gets MACK Feb 26 and will prep reagents, generate mission script, run sub-protocol tests&nbsp;
# One month cold test of Mack w/ his new valves/hand starting Mar 7.
## OBJECTIVE:&nbsp; get through a full carousel of pucks; run it hard to make Mar 24 preparation
# Once Mack finished with box test, we replace with Bruce for box test.
## Once Mack into box testing, we schedule ship dates.
# Prep for Spring deployments (Mar 24 \-->Mar 30){color:#ff0000}{*}Deploy{*}{color} MACK (March 31-Shana Rae)
## {color:#0000ff}{*}Recover{*}{color} MACK Apr 17, {color:#ff0000}{*}Deploy{*}{color} BRUCE \-\- Shana Rae
# &nbsp;{color:#0000ff}{*}Recover{*}{color} BRUCE, {color:#ff0000}{*}Deploy{*}{color} MACK (May 1 \-\- Zephyr)
# {color:#0000ff}{*}Recover{*}{color} BRUCE (May 27), {color:#ff0000}{*}Deploy{*}{color} *both* MACK and NEO (May 28 \-\- Zephyr)
# End mission Jun 30.

Dates after March 31 Shana Rae are flexible, until Zephyr takes over....]]></property>
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<property name="body"><![CDATA[Present: Chris S., Scott, Kevin, Jim, Doug, Wayne, Addie

Absent: Cheri, Brent

h3. Deployment Update

* Thanks to all on an awesome deployment
* Post-can QC:
** Bruce has a leak, so images not looking good.&nbsp; South Carolina wants to do some tests; if we can do in 1 week great, otherwise should send their reagents back.&nbsp; Cheri back on Monday and will work on finding leak.
** Errors during deployment:
** Bruce: puck failed to go to camera seal
** Bruce: developed leak on processing side
** Mack: error on removing flush puck from garage
&nbsp;
* Chris & Scott will work on tracking down the bad puck Bruce had during the deployment to see if there's a smoking gun...
&nbsp;

h3. Machine Builds

* harmonic drive has been running all week; working better, but Scott needs to check it more closely.&nbsp;

h3. MFB

* &nbsp;Addie: wil check with Jose about status of voltage regulator boards
* 64MB host boards (4) ordered; host ribbon cables ordered
* Lots of work for Jose that may require formal work request.&nbsp; Jim will check with Mark Brown
** measuring for wire harness; MBARI will build 2, rest will be sent out
** after these measurements, Jose/Scott will do schematic
** Jose will also be involved with serial connector to PCR builds and making 1 connector joining Grill to core or to stand-alone power supply.
* Jim will contact LLNL about January PCR module delivery
* NAMING CONVENTION:&nbsp; Grills will be sequentially numbered starting with MFB01.&nbsp; Subsequent will be MFB02, MFB03, MFB04, etc.

h3. Software

* &nbsp;If we decide to roll-out new Ruby code, it is better to do earlier than later as we'll need a stable platform by March.&nbsp; Must meet with Brent for debugging NEO results.
* See 2009 schedule below:

h3. DWSM


h6. +Sphere+

* &nbsp;Roughly 2 weeks machining left
** bottom is off lathe and in mill; finishing ports
** top is in lathe; found a void--worried there may be others.&nbsp; Waiting on X-ray quote from Tapemation.&nbsp; Doug to notify Wah Chang, who may be responsible for repair.
* will be using vulcanized assembled O-rings @ $15/each.
* Fasteners to be ordered--Ti vs. SS; still getting prices and lead times, but whether we go on Northern expedition or go on MARS will influence which we purchase
* bulkhead penetrations still to be made in-house;&nbsp; will talk to Scott about min-K connectors
* Where will sphere sit upon delivery? Will ask about back of Larry's space or storing in high-bay.

h6. +DWSM+

* Build has begun; currently waiting on Dean's valve parts
* much testing can be done with current dwarves; all boards for testing are available through Dick.

h3. GUI Development

* GUI is now parsing data.&nbsp; Kevin wants to store in Alfresco since this is accessible via the web to outsiders without having to give out MBARI accounts.

h3. Other Items:

* Bldg B lab will eventually need cleaning; Doug has his space along east wall; center will be where cores sit.&nbsp;

*{+}2009 deployment schedule looks like this :+*
* Winter/Spring \-\- series of DWSM/sphere test deployments.&nbsp; Last will be a Flyer deployment (5 days?), then several week break, then Northern Expedition in July.
* &nbsp;Spring \-\- series of S. California pier deployments; dates and lengths flexible, but likely 3 machines in three different cities for 1 month
* End of 2009 \-\- MARS deployment
* &nbsp;Above could change if N. Expedition gets canceled due to budget issues.&nbsp; Will know more after Nov. 13 Packard Board mtg.]]></property>
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<property name="body"><![CDATA[h1. WHOI / NSF-MRI kickoff meeting

Present:&nbsp; Rich Schramm, Kevin Gomes, Brent Roman, Jim Birch

Absent: Brian Schlining\\

h4. Discussion Items:

# &nbsp;Goal is to create a 'state' vector which polls the instrument and creates a vector of current state of all relevant entities.&nbsp; Brent to work with Rich to create this de novo.
# Rich's software will read this vector and move his animations accordingly
# Kevin working on populating this state vector from the log file.
# An issue with the animation software is the preciousness of screen real-estate.&nbsp; Thus, what views need to go together?&nbsp; Like carousel and hand, or hand and rotary valve...?
# Needed to talk about how to animate the fluidics diagram.
## Animation preference is in this order;
### fluidics diagram
### happenings on the deck
### bag fluid levels

h5. Image Analysis

&nbsp;Brian working on 3 files with fiducials to try and completely automate the alignment and analysis.&nbsp; Also working on a calibration curve of the intensity data.&nbsp; Roman needs to print another set of arrays for him.&nbsp; Brian said he'd look at the 2 sets before next week.]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 21, 2008*

*11am-12*
Present: Jim, Doug, Chris S., Addie, Cheri, Kevin G.

LATEST Deployment Schedule is [HERE|ESPAPP:2008 Q1-Q2 Schedule (rev 5)].&nbsp;

h3. Tech Transfer


h6. Discussion Items:

* Update on Mack progress
** {color:#339999}Cheri noticed on Tuesday (19th) that the compression bolts are not gripping the motor shafts tightly enough.&nbsp; This stopped all preparation for the mock-mission run, and demanded a re-design of the valve/motor connection, which Doug helped brainstorm and propose a solution.&nbsp; 2mm balls are required for the fix, and, after calling every ball bearing place in 3 counties, we had to rely on MacMaster (delivered today).{color}

* &nbsp;Mike Parker contacted about piezoprinter problems (holding down membrane, cutting out disks) and is designing solutions.&nbsp; Also will be approached about a puck holder.

* New syringes.
** {color:#339999}Still not heard back from company{color}

* Screens and scintered frits
* &nbsp;
** {color:#339999}CE metalurgical will create a 'stamp' to label the frits.&nbsp; Cost is $300/tool.&nbsp; Will label at 1/2radius on one side of frit.{color}

* Puck Laser Etching
** {color:#339999}Mike put in SAF bottom holes, but got confirmation from El Camino on remaining pucks to not forget that again.&nbsp; Remaining pucks from first batch ready for etching.&nbsp; Then to send out lot3 for etching.&nbsp; Have spoken to Roman and Nilo about this.&nbsp;{color}

h3. MFB

Discussion Items:

&nbsp;After seasoning the tube, gels show that we are getting product produced (using calf thymus).&nbsp; Addie will begin work for the Moore year-end report.

h3. Software

* puck heating control
** {color:#339999}Brent has gotten calibration w/in 4degrees, but measuring puck temp is problematic.{color}
* Firmware 'lock-down'?
** Thermal boards and Dwarf boards look fine, but the failing home sensor in the hand seems to generate a cascade of failures.&nbsp; This will be fixed.(Brent)
** GG and Neo will have old firmware and old Ruby.&nbsp; Mack will use newer of each and these versions need to be kept separate.

h3. Sphere and 4K DWSMS

* Sphere update
** {color:#339999}No word or update from Wah Chang.{color}

* DWSM progress?
** {color:#339999}Doug believes he's found a pump that will push reliable, reproducible amounts of fluid.&nbsp; Ordering motor to run it, and now must test that it pushes the correct volumes of fluids with no back-flow.{color}
* Battery boxes?&nbsp; {color:#339999}Will order 1 box (~$2200; acct 701312.04; Scott){color}

ACTION:&nbsp; Have BATTERIES been ordered? (Jose)
ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)&nbsp;

h3. GUI Development

* Mission script GUI introduction

Kevin has placed new GUI on the server here.&nbsp; Rich Schramm available to do data parsing work; we want to utilize this by Sept deployment.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.]]></property>
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{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| | G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| 1 \\ | Ambient Flush Reservoir \\ | * Mixtures, chemicals?
* Volume (s)
* Material compatibility
* Dilution with SW?
* Flush fluids as well? | | \\ | 1 |
| 2 | Intake point and Screen \\ | * Single intake?
* CU screens?
* Location on LRAUV
* Min bore size? | | | 2 |
| 3 | | | | | |
| 4 | Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * Number of ports (intakes and ambient storage)?
* 3-way valve
* Min bore size?
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| 5 | Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi
* Min bore size?
* Non-corroding
* Fail closed
* Wattage? Power budget?
* Small scale, Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| 6 | Cartridge Selection valves \\ | * Chemical suitable
* 500 psi
* Min bore size?
* low power
* flush free | * Ladder/Looper options
* 2 position spool valves
* Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| 7 | Cartridge Return Array \\ | | * check valve
* part of Selection valve
*  | * LeeCo
* Parker | 4 |
| 8 | Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
* Testing process, procedure
* Vibration testing? | * Dibafit
* Upchurch
* LeeCo | 1 |
| 9 | Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| 10 | Filter selection valving \\
(transition from sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | * Rotary valve, reagent select, part of filter holder
*  | | 4 |
| 11 | Cartridge Seals \\ | Connection between spool valves, cartridges to cartridge\\ | | | 2 |
| 12 | \\ | | | | |
| 13 | \\ | \\ | \\ | | |
| 14 | Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| 15 | Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| 16 | Filter Evacuate \\ | * Need to remove seawater <5% of lysis volume.
* In G2, remaining seawater needs to be <100uL
* For 1mL lysis volume, <50uL, or <1 drop.
** Test numbers: Dry filter \+holder, 9.91g
** wet filter (filter holder dry) 9.95g (40 uL)
** no change if vacuumed, no change w/ singe 10ml blow thru
** after 3X 10mL blow thru, 9.92g (10 uL)
** filter appeared to be mostly dry | * Air pressure evac (G2 method)
* Vacuum assist below filter?
* Filter holder is piston assembly, w/ small dead volumes
* Displacement with other fluid? | | 4 |
| 17 | Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| 18 | DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| 19 | Direct Capture \\ | | | | |
| 20 | Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| 21 | Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| 22 | | | | | |
| 23 | Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| 24 | Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| 25 | Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| 26 | Cartridge Actuators \\ | | | | 4 |
| 27 | \\ | \\ | \\ | \\ | |
| 28 | Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| 29 | Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| 30 | | | | | |
| 31 | TRANSFER TO AM | | | | |
| 32 | Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| 33 | AM Selector Injection Loop \\ | | | | 4 \\ |
| 34 | Clean Injection Loop \\ | | | | 4 \\ |
| 35 | Rotor Pass-Thru \\ | | | | 2 |
| 36 | LRAUV Platform Interface \\ | | | | 2 \\ |
| 37 | LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | See model \\
G3LRAUVHousing.sldasm \\ | 2 \\ |
| 38 | | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.

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\\
# [Sep 15]]]></property>
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<property name="body"><![CDATA[Present: Jim, Scott, Doug, Bruce K., Roman, Brent


Absent: Chris S., Chris P, Julie, John R.


h3. Issues:

* BIOSPACE DEPLOYMENT.
** Deployments went well.&nbsp; All machines around 7m deep.&nbsp; 4-band bungee seems much more stretchy (Bruce at SC site).
** SC site is 11.5 miles from Abe's house, thus had to use Brent's shore station.&nbsp; 3-6 feet more of antenna would really help.
** Some discussion of WHOI's idea of radio testing Oct 13-15 when Bruce on cruise
** Brent set up 'seeds' that all pulling down mid-res images and file copying from instruments to shore stations.
*** h5. +Machines and first day of mission+



h6. Bruce

had problem with SH1.&nbsp; either air in line or blue frit.&nbsp; used lyfill to flush intake, and then retried and it ran it's first SH1.&nbsp; Bruce has old CTD (that used to corrupt HEX files but is working okay right now) and old driver.

h6. Mack

Mack as newer CTD but started with old driver.&nbsp; Miscommunication; thought Mack would have old CTD.&nbsp; Brent pushed down updated code (with new driver).&nbsp; This has not been QC'd...

h6. MOE

first IPC looked good. second failed.&nbsp; Third looked good.&nbsp; Arrays are black.&nbsp; multiple reasons why this could be but bottom line; *not enough QC*.

* D-ESP
** Parts for new IEP will arrive by next Thursday.
** Plan:
*** Install IEP {color:#ff0000}Oct 12{color}
*** Load Reagents {color:#ff0000}Oct 21{color} then begin testing
*** Seal DWSM {color:#ff0000}Nov 3-4{color}.&nbsp; High pressure testing during/after.
*** Sphere closed {color:#ff0000}Nov 17{color}
** Brent will need to modify firmware to get pump into dwarf port(?)
** Went over Scott's to-do list; he's gone until Oct 25.
** D-ISUS--when will it be ready?&nbsp; It will run off battery pack, and this Dec we'll use Luke's Al housing.&nbsp; Do they want Ti housings?&nbsp; We need to order.
*** 2 months on this ISUS housing build.
* Bruce K brought up temp issue in GOM.&nbsp; Much discussion, no resolution.



h4. G3 planning

* Team needs as much info as possible before Nov 11,12 requirements meeting.&nbsp; What are goals, who will be presenting, schedule of the day should go to team ASAP.]]></property>
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<property name="body"><![CDATA[Triple Deployment Sept 28-Nov 3

Weight calcs as follows:
|| All in lbs \\ || || diff || ||
| Mooring wt (can & anchor) in air \\ | 1314 | | |
| Mooring wt w/anchor in water \\ | 1205 | 109 | |
| Can weight in air \\ | 754 | | |
| Anchor wt in air (1314-754) \\ | 560 | | |
| Anchor wt in water (560-109) \\ | 451 | | |
| Mooring wt (can & anchor) in water \\ | 297 \\ | | |
| Buoyancy of mooring (451-297) \\ | 154 | | |
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 14, 2008*

*11am-12*
Present: Jim, Doug, Chris S., Addie, Scott, Brent, Cheri, Rich S., Kevin G.

LATEST Deployment Schedule is [HERE|ESPAPP:2008 Q1-Q2 Schedule (rev 4)].&nbsp;

h3. Tech Transfer


h6. Discussion Items:

* Update on Mack progress
** {color:#339999}Have run into a hand homing issue.&nbsp; Replacement of everything, and movement of hand to another instrument has the issue following the hand.&nbsp; A new hand on Mack does not show this problem, but still unknown what is causing it.&nbsp; Otherwise, everything calibrated on Mack (hand, intake pressures, carousal).&nbsp;{color}
** {color:#339999}Dynamic control of puck temperatures is good, but still only able to hold within 4 degrees of setpoint.&nbsp; Most likely because temp sensor doesn't touch puck all that well, or this touching varies; thus final goal temperature is off.&nbsp; Regardless, Brent thinks we are much better than the GG and Neo runs last year.{color}
** {color:#339999}With the long weekend (Friday and Monday-Prez day) we will run non-stop mock missions through Mack (Flush, BAC, LARV,HAB, HAB-DA), before bagging on Tuesday and allowing science to run 'real' missions.&nbsp; Deployment schedule has changed (see above link).{color}

Chris' plan for the long weekend mock:
| Hi everyone - \\
\\
target temps are ideally: \\
\\
sh1 - 85C \\
DA - 70C \\
sh2 (laf, saf) - 30C \\
\\
having said that, we might we drop the actual setting on the esp a couple degrees to remain on the safer side of the line (hotter is worse).&nbsp; So Brent, use your judgement.&nbsp; I know a setting of e.g. 28 for sh2 sould be hard to hit when working in a warmish room, but worth a try? \\
\\
The outline of the simple&nbsp; mission for the faux run is given below.&nbsp; All sample vols should be 50 ml (sample for lysis and wcr).&nbsp; All reagent lines, including sample) will be filled with flush fluid.&nbsp; Exposures should be 160s 1x1, 40s 2x2, auto 2x2.&nbsp; Should we #-out the auto exp since there should be no light, or just let it burn till time-out for kicks? \\
\\
\\
\# before starting run prime all reagent lines and make sure to purge intake so the sample line is primed too. \\
\\
romanFlush&nbsp; #not sure this syntax is correct - Ro pls verify \\
bac \\
larv \\
hab \\
habda \\
da \\
\\
\#end \\
\\
this should be 22 pucks \-\- do you want to put them in a single stack or spread around? \\
\\ |
* &nbsp;Mike Parker contacted about piezoprinter problems (holding down membrane, cutting out disks) and is designing solutions.&nbsp; Also will be approached about a puck holder.

* New syringes.
** {color:#339999}Still not heard back from company{color}

* Screens and scintered frits
** {color:#339999}Will order 400 10um frits with frit packing tool. total cost $4300.00.&nbsp;{color} {color:#0000ff}Order placed 2-14-08{color}{color:#339999}.&nbsp; Here is the{color} [order|^MBARI PO-0810358.pdf] {color:}and the{color} [quote.|^mbari82024E021308.doc]
** {color:#339999}We will order enough screens for 6 instruments.&nbsp; (who is doing this?){color}

* Puck Laser Etching
** {color:#339999}first half of pucks have returned from the etching, and SH1 tops and HV puck tops are mislabled.&nbsp; Will investigate sending these back, as well as sending out the 2nd batch of lot2 pucks.&nbsp; The first 'new' batch (lot3) has arrived from El Camino, Mike P is inspecting.&nbsp; Has found they forgot to put hole in SAF bottoms.&nbsp; Will return to get that done.&nbsp; These pucks will go straight to etching before we&nbsp; get them.{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose still working to assemble a more accurate list of electronics/machine for a more accurate cost estimate

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

h3. MFB

Discussion Items:

&nbsp;Decided&nbsp; to run thermal cycler all weekend with just water and bleach, to see if extra 'seasoning' of the tubing will lessen its inhibition of the PCR reaction.&nbsp; Upon return next week, will run sample to test PCR effectivness.

ACTION:&nbsp; Addie to look at heating profile times to make sure we are not cooking our reaction. (Addie)&nbsp; {color:#0000ff}Finished{color}

h3. Software

* puck heating control
** {color:#339999}Brent has gotten calibration w/in 4degrees, but measuring puck temp is problematic.{color}
* Firmware 'lock-down'?
** Thermal boards and Dwarf boards look fine, but the failing home sensor in the hand seems to generate a cascade of failures.&nbsp; This will be fixed.(Brent)
** GG and Neo will have old firmware and old Ruby.&nbsp; Mack will use newer of each and these versions need to be kept separate.

h3. Sphere and 4K DWSMS

* Sphere update
** {color:#339999}No word or update from Wah Chang.{color}

* DWSM progress?
** {color:#339999}Doug believes he's found a pump that will push reliable, reproducible amounts of fluid.&nbsp; Ordering motor to run it, and now must test that it pushes the correct volumes of fluids with no back-flow.{color}
* Battery boxes?&nbsp; {color:#339999}Will order 1 box (~$2200; acct 701312.04; Scott){color}

ACTION:&nbsp; Have BATTERIES been ordered? (Jose)
ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)&nbsp;

h3. GUI Development

* Mission script GUI introduction

Kevin has placed new GUI on the server here.&nbsp; Rich Schramm available to do data parsing work; we want to utilize this by Sept deployment.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
\\
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<property name="body"><![CDATA[SLAS 2012 San Diego

Enabling Technologies for G3 ESP

# Microsonic      Systems, San Jose Conact Vibhu Vivek (Pres, CEO)-TALK http://www.microsonics.com/technology.html Fresnel Annal Sector Actuator (FASA) create lateral waves w/o cavitation.&nbsp; At different strengths can mix (in layers), shear or lyse.&nbsp; Have a Phase 1 SBIR Grant (NASA) .&nbsp; Also developing hybrid power devices to recapture energy used in the process.&nbsp; Very interested in working with us.
# Ifast      One Step Analyte Technology David Bebee&nbsp; \-TALK http://www.ncbi.nlm.nih.gov/m/pubmed/21423999/
# Pall      Life Sciences Galina Formovska (Sr. Principal Scientist)&nbsp; Access to bulk membrane compatible with      Qiagen buffers, if OEM Qiagen does not work.&nbsp;
# ThinXXS      Germany\- Asked if incorporated bead beating to custom made chips... "Could      not discuss."
# MiniFAB-design      integration and manufacture of polymer micro and nano systems. Australia
# Proteomic      Technology-Mark Chee (Prognosys Biosciences)-TALK Design Protien in silico\- Synthesize DNA\-Peptide-DNA library\-assay\-sequence Example:&nbsp; Look for protease cleaving sites.&nbsp; Peptide portion of Peptide-DNA construct imobolized.&nbsp;Introduce protease.&nbsp; Those with Protease sites are cleaved freeing the DNA side of the contruct.&nbsp; Those are collected and sequenced. Imagine spotting Peptide-DNA constructs on Array, expose.&nbsp; Rather than sequencing, probe the array for what is left.&nbsp;
# &nbsp;Application      of Panomics Assay (like our SHA) on hydrogel particles (250uM) Novartis      Adam Hill.&nbsp; Section of the particle      contained a barcode and multiplex for different captures.&nbsp; With camera has up 10um resolution.&nbsp; After sandwich, sent the particles down      microchip and imaged with camera.
# &nbsp;LUCAS      (Lens Free Camera).&nbsp; (Aydogan      Ozcan)&nbsp; 10-20cm2      holographic/fluorescent images.&nbsp; Runs on LEDs could get down to low um resolution and keep the same      field of view (Wide Field Fluorescence).&nbsp; Run on smart phone.&nbsp; Used      software to recreate images:&nbsp; fluorescene arrays, Giardia, E.coli, RBCs infected with Plasmodium,      etc..&nbsp;&nbsp;
# Motion      and Control
## Pro-Dex       (www.pro-dex.com) has multi axis       motion controllers
## Trinamic       (www.trinamic.com ) also does       motion and specializes in incorporating their chips into other custom       boards.
## ELMO       has a new line of controllers, "gold" line
# Valve
## Burkert       has a couple valves that have hit-and-hold circuitry built into the       valve.
## Clippard       has a line of diaphragm valves that may be interesting. Typically used in       pneumatics. www.clippard.com
## VICI
## Valcor       valves
# Fittings
## Dibafit       has some fittings that can handle high pressures.
## VICI       does as well.]]></property>
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<property name="body"><![CDATA[h2. Outline of instrument plan for Jan-Jun, 2008

Mack has been cold tested with new hand and new valves and Roman Flush run to check tubing.

Temp calibration Jan 29-Feb 11.

Science gets MACK Feb 11 and will prep reagents, generate mission script, run sub-protocol tests&nbsp;
# One month cold test of Mack w/ his new valves/hand starting Feb 19 (this is earliest possible day).
## OBJECTIVE:&nbsp; get through a full carousel of pucks
## test should last most of 4 weeks (although 3 weeks would be acceptable)
# March 11 is earliest we pull and deem a success.&nbsp; Once pulled, we replace with Bruce for box test.
### Once Mack into box testing, we schedule ship dates.
# Prep for Spring deployments (Mar 14 \-->Mar 19)&nbsp; These dates may slip.
# {color:#ff0000}{*}Deploy{*}{color} MACK (March 20-Shana Rae)
## {color:#0000ff}{*}Recover{*}{color} MACK Apr 10, {color:#ff0000}{*}Deploy{*}{color} BRUCE \-\- Shana Rae
# &nbsp;{color:#0000ff}{*}Recover{*}{color} BRUCE, {color:#ff0000}{*}Deploy{*}{color} MACK (May 1 \-\- Zephyr)
# {color:#0000ff}{*}Recover{*}{color} BRUCE (May 27), {color:#ff0000}{*}Deploy{*}{color} *both* MACK and NEO (May 28 \-\- Zephyr)
# End mission Jun 30.
\\]]></property>
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<property name="body"><![CDATA[h1. ESP 'Science' Meeting


h4. Cawthron


Trial Deployment
* We will do a 'trial' deployment of new mooring to test before Cawthron.&nbsp; Initially trying for week of Feb 27 using Shana Rae.&nbsp; Scott leading this.&nbsp; Jim Christman has been emailed to ask about dates (2-13).

Communications
* GSM does not support incoming data on their networks.&nbsp; Brent has two possible solutions for data transfer that he's working on.

Deployment support
* Kevan and Chris P getting reagent list together.

h4. &nbsp;CANON Cruise

* Still unclear if drifter should be deeper than 25m.
* Will oxygen sensor be necessary?
* CANON meeting Feb 16 should answer these questions

h4. 3G planning

* &nbsp;We will be doing dead-end filtration, although types of filters depends on volume and bugs.&nbsp; All extractions have been on Durapore; haven't tested Supore.
* Bead beating is best for RNA and DNA extraction;&nbsp; works best at room temp--have not tested yet at cold.
** all testing has been on ribosomal targets.&nbsp; Started testing functional genes, and 2 tested so far are in very low abundance.&nbsp; Now waiting to get more from Vanessa.
** All-Prep kits outperforms all others at overall nucleic acid extraction.&nbsp; Does better at DNA than DNeasy, but RNeasy gets more RNA than all-prep.
* At Lab Automation next week look at two things:
** filtration and lysing in same step.&nbsp; CAn be done on same filter?
** look for how people move fluids around.&nbsp; Important for size fractionation, filtering of lysate, etc...
* Much discussion about who 'owns' the injection loop to analytical module.
** What volume needs passing?&nbsp; is it fixed, or could it be different depending on module needs?&nbsp; must we 'condition' the sample before handing it off?&nbsp; who cleans the loop?
* Our sample volume and how we break things really sets us apart.&nbsp; After that, the extraction and handling is very similar to the rest of industry.]]></property>
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# [Jan 31]
# [Feb  2]
# [Feb 14]]]></property>
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<property name="body"><![CDATA[h1. ESP 'Science' Mtg


h4. Frackers

# Found that RNA quality is good enough to run microarrays; RIN numbers look good, but still unsure if 'bad' numbers would result in poor microarray results.&nbsp; Unclear what the future is with these results.
# Current extraction testing has been on 16s gene; must test functional genes and chris P getting p/p for rbcl, AOAa, and Roseobacter.&nbsp; Hope to have two finished this week.&nbsp; If these work, Chris has multitude of questions to move forward.&nbsp; Looks like enzymatic lysis will not work for RNA; works great for DNA, but too slow for RNA, allowing RNAses in to destroy RNA before complete lysis.
# Elif has finished standard curves for pier deployment and is now crunching the numbers.
# Gordon
## almost completely cleaned.&nbsp; Seems like o-rings are culprits with 10^4 DNA copies hanging out in the top and 10^3 in bottom on collection(?) side.
## NEO
### same issues.&nbsp; Roman has helped develop a cleaning protocol, and we now know where to look first when heavily contaminated.
# To run BASIC event detection (i.e., threshold crossing) Brent needs to test the new Ruby interpreter.&nbsp; This will be installed on NEO this week after Roman fixes bearing and leak.

h4. Particle Concentrators

# &nbsp;Still waiting to hear from Kia.&nbsp; Jim will ping him.
# We have settled on dead-end filtration, but may not be constrained to circular form factor, just similar surface area.
# Is size-fractionation still a requirment?&nbsp; Yes.&nbsp; it is one of our three operational-use scenario.

h4. Cawthron Deployment

# Email sent to Chris Cornelisen.&nbsp; Ideas:
## deployment will be May 1-31, 2012
## must get two cores to Cawthron by April 2 to have time for set-up.
## Kevan has sent list of targets we are proposing to go with.
## MBARI will be paying for reagents/assays, but Cawthron should buy directly from Spyglass to mitigate customs issues.
## post-deployment runs to be performed AT Cawthron.
## Doug developing a shipping option for the cores which will be 'dry-shipped' via air freight.
# We have only 1 ISUS and it will be going to NZ.

h4. Other Items

# &nbsp;Do we need permits to put ESP on pier in Newport Beach/Orange County?
# Passports--everyone check that your's are up-to-date.&nbsp; Kevan has checked and Visa is not needed for New Zealand.
# We need some hard dates related to G3 development so people can plan their lives, and we can work development around the many deployments.
# Need to find out what depth Drifter needs to be at for Sept CANON cruise.&nbsp; Currently have 1 25m cable.&nbsp; If they want an oxygen sensor on CTD, they should buy (or we'll split it with them)
# We are having 4 E/M cables made.&nbsp; Two 15m (finished) and two 25m (in que to be built)]]></property>
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<property name="body"><![CDATA[h3. Outline of instrument plan for Jan-Jun, 2008

Mack has been cold tested with new hand and new valves and Roman Flush run to check tubing.

Science gets MACK Feb 19 and will prep reagents, generate mission script, run sub-protocol tests&nbsp;
# One month cold test of Mack w/ his new valves/hand starting Feb 25 (this is earliest possible day).
## OBJECTIVE:&nbsp; get through a full carousel of pucks
## test should last most of 3 weeks
# March 17 is earliest we pull and deem a success.&nbsp; Once pulled, we replace with Bruce for box test.
### Once Mack into box testing, we schedule ship dates.
# Prep for Spring deployments (Mar 17 \-->Mar 30)
# {color:#ff0000}{*}Deploy{*}{color} MACK (March 31-Shana Rae)
## {color:#0000ff}{*}Recover{*}{color} MACK Apr 17, {color:#ff0000}{*}Deploy{*}{color} BRUCE \-\- Shana Rae
# &nbsp;{color:#0000ff}{*}Recover{*}{color} BRUCE, {color:#ff0000}{*}Deploy{*}{color} MACK (May 1 \-\- Zephyr)
# {color:#0000ff}{*}Recover{*}{color} BRUCE (May 27), {color:#ff0000}{*}Deploy{*}{color} *both* MACK and NEO (May 28 \-\- Zephyr)
# End mission Jun 30.

Dates after March 31 Shana Rae are flexible, until Zephyr takes over....]]></property>
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<property name="body"><![CDATA[Present: Cheri, Scott, Doug, Brent, Jim

Absent:&nbsp; Chris S.

h3. Machine Builds

* PCB's for a core build have been sent to McLane.&nbsp; Scott working on cost calculation to send them.
* Doug has first Ti HV puck tops.&nbsp; Will work with Roman on whether they are appropriate.
* Screen drawings have been modified so holes are smaller (=stiffer metal).&nbsp; Must compare to PO drawings to find most recent.
* Cheri tasked with assembling a 'spare' kit and we will get this&nbsp; x3

h3. MFB&nbsp;


h3. Drifter


h3. Software


h3. Deep ESP/DWSM

* Over weekend, water was inadvertently let into the sphere (~500ml) due to the wrong puck (LAF) being loaded.&nbsp; All things looked okay, until we tried the next SH1, and the puck heater started giving wild readings.&nbsp; It is probably fried.&nbsp; We will run some core negative PCRs, and recover next week (Tuesday) if weather permits.

h3. GUI


h3. Deployment Issues

* Brent working on networking the pier deployment.&nbsp; Will acquire larger antenna(s) and working on VPN issues.&nbsp; Possible trip down there Weds.&nbsp; Deployment looking to be during the week of the 19th.
* Doug will talk to science about designing the Pier-water Introduction System (PIS).

h3. &nbsp;Other Items

* Harbans Dhadwal (Stoney Brook, NY) will be&nbsp; visiting Friday, Oct 30.&nbsp; He'll be learning about basic MFB functions.&nbsp; Will need a 'cheat sheet' of commands, and maybe the 'training' can used colored water.&nbsp; Cheri on this.]]></property>
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<property name="body"><![CDATA[h3. Minutes from Mock Mission Planning Meeting


h5. Questions

# How are volumes for duplicate phases handled?
{noformat}
# Sample Volumes for Assay Types
$habVol=1000
$larvVol=900
$larvVol=700
$daVol=30

startTube 2
# require '08feb'


startAt "14:44:34 03/12/2008"

initialPurge
hab
napUntil "10:05:13 03/13/2008"

larv
napUntil "05:50:00 03/14/2008"

initialPurge
larv
napUntil "17:45:00 03/14/2008"

da
shutdown
{noformat}
# Script gets generated but not in sync with timing of simulator/instrument, how to best synch:
{noformat}
CH.stop
I2C::MsgErr in sampler -- I2C::Servo::OffCmd Not yet modeled
I2C::MsgErr in storage -- I2C::Servo::OffCmd Not yet modeled
I2C::MsgErr in sampler -- I2C::Servo::ConfigureCmd Not yet modeled
I2C::MsgErr in storage -- I2C::Servo::ConfigureCmd Not yet modeled
CH.configure CHconfig
PH.stop
PH.configure PHconfig
Posix::Error in quick -- /dev/ctd not a character device
Starting with tube #2
delayUntil "06:15:00.00 PDT 13-Mar-08"
@06:15:00.00PDT13-Mar-08 <poll> CTD.startLogging
@06:15:00.00 <quick> Initial Intake Purge
@06:16:30.00 ==> hab 1000ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@09:46:30.00 Disinfect Intake
@09:48:30.00 Shutdown
delayUntil "13:50:00.00"
@12:15:00.00 <poll> CTD.update
@13:50:00.00 <quick> ==> bac 900ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@17:20:00.00 Disinfect Intake
@17:22:00.00 Shutdown
delayUntil "01:25:00.00 PDT 14-Mar-08"
@18:15:00.00 <poll> CTD.update
@00:15:00.00PDT14-Mar-08 CTD.update
@01:25:00.00 <quick> Initial Intake Purge
@01:26:30.00 ==> larv 900ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@04:56:30.00 Disinfect Intake
@04:58:30.00 Shutdown
delayUntil "11:20:00.00"
@06:15:00.00 <poll> CTD.update
@11:20:00.00 <quick> Initial Intake Purge
@11:21:30.00 ==> da 1000ml, :image=>[:hires, 15, :default, 4, :midres, :auto]
@12:15:00.00 <poll> CTD.update
@14:21:30.00 <quick> Disinfect Intake
@14:23:30.00 Shutdown
delayUntil "20:30:00.00"
@18:15:00.00 <poll> CTD.update
@20:30:00.00 <quick> Initial Intake Purge
@20:31:30.00 ==> hab 1000ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@00:01:30.00PDT15-Mar-08 ==> da 1000ml, :image=>[:hires, 15, :default, 4, :midres, :auto]
@00:15:00.00 <poll> CTD.update
@02:01:30.00 <quick> Disinfect Intake
@02:03:30.00 Shutdown
gui_test.rb Assays Completed. CTD logging continues ... 
delayUntil "00:13:07.00"
Schedule::Error in quick -- Delay::RunEvent for @00:13:07.00 PDT 15-Mar-08 is in the past
Waiting to Resume from Checkpoint "gui_test.rb Assays Completed. CTD logging continues ... "
@06:15:00.00 <poll> CTD.update
@12:15:00.00 CTD.update
@18:15:00.00 CTD.update
@00:15:00.00PDT16-Mar-08 CTD.update
{noformat}

{panel:title=New Requests}
# Have capability to add comments to phases that show up in script. Maybe go out in log too. Also add header comments. (global too).
# Modify protocol so it doesn't kill between phases (want capability to call out alternate purge).
# Always odd things (give it ruby and time to run and it puts it in script).
# Phases should be different colors
# BUG: If delete last phase, can't add one at end.
# Need to specify a way just to sequence things, not deterministic time. Or say, I just want to wait 15 minutes after it finishes.
# Have way to call out initial purge instead of upper/lowercase
{panel}
]]></property>
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<property name="body"><![CDATA[D-ESP get retrieved October 27, 2009 and re-deployed November 25, 2009.

&nbsp;Below, add to the list of 'to-dos' before the November deployment back on MARS:
# Complete integration of Data Aqcuisition subsystem
# Ground Fault subsystem
# Remote Host reset]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Mar 13, 2008*

*11:00 am* MBARI: Birch, Scholin, Jensen, Roman

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; LLNL: Dzenitis, Bennett, Riot, Dean (?);&nbsp; Tony absent
&nbsp;

h3. Teleconferences with LLNL



h6.

John feels MFB development has 3 stages:
# Make right what we already have; this is in the original scope of work of what we want
# Finalize some things before the last design
## analog boards need final (correct) values
## finalize the optics
## some heater tubing does not slide in easily; fix heater element
## minor changes in circuit board structure
## incorporate better connectors
## better machine heater cover package
# How do we make many of them?&nbsp; This ranges from
## LLN makes more of what they finalize
## specialty shops do subcontract work--subassemblies go to MBARI or LLNL for final assembly and checkout
## contract outside to make the blocks

LLNL wants +out+ of the manufacturing loop.&nbsp; They are leaning toward

&nbsp;Subcontractors build subassemblies and we put together and test according to LLNL procedures.&nbsp; LLNL will put together the testing procedure.\\

Chris says we need 8 blocks.

&nbsp;During documentation of the assembly, if we assumed more active role in documentation of assembly and testing procedure, it would lower the cost.

John wonders if thermal profile is still rock-solid?&nbsp; We will get Addie to run one and provide ASAP.

&nbsp;He hopes to have SOW for additional work in 1 week.
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<property name="body"><![CDATA[Draft ESP cheatsheet as of 3/21/07

This will likely need to be put into a Word document.
Feedback appreciated...

\-----------\-


*Avoiding a position* on a rotary valve example------> &nbsp; &nbsp; &nbsp; PTV.to :puck, :avoiding=>:PRV &nbsp;\\

Preparation for running high level protocols in the lab:

0) Insure that no one else has is running the esp
&nbsp;&nbsp; application on the ESPhost machine

1)&nbsp; ssh to the ESPhost machine as the appropriate user
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (most often this will be user esp or scholin)
$ ssh user@espHost

2)&nbsp; confirm the ESP is getting the right code base
&nbsp;&nbsp;&nbsp; check the Using ... line that appears right after the login
&nbsp;&nbsp;&nbsp; It should say
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Using esp@espbook, ESPhome=/home/esp/esp2 for user scholin
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; or
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Using esp2local, ESPhome=/home/esp/esp2 for user esp

&nbsp;&nbsp;&nbsp; The message:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; WARNING:&nbsp; ESPhome is undefined\!

&nbsp;&nbsp;&nbsp; indicates a transient network filesystem problem (NFS).
&nbsp;&nbsp;&nbsp; If the machine is in a safe state, simply logout, cycle its
&nbsp;&nbsp;&nbsp; power and try again after 30 seconds or so.&nbsp; Alternatively,
&nbsp;&nbsp;&nbsp; you can login as the root use and type:

\# service nfsmount start

&nbsp;&nbsp;&nbsp; After the nfsmounts all complete, logout of root and
&nbsp;&nbsp;&nbsp; try logging in as scholin
&nbsp;&nbsp;&nbsp; again.&nbsp; You should not see this problem when logging in
&nbsp;&nbsp;&nbsp; as user esp, as this user does not rely on NFS mounts.

3)&nbsp; start the esp application

$ esp

4)&nbsp; Insure that the ESP is homed and ready:

esp>&nbsp; ESP.ready\!

5)&nbsp; Visually verify that the FlushPuck is in its garage.

Now, after loading the appropriate puck(s),
you will be ready to run your protocols as follows:

\[Whole Cell Archive\]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; wcr sampleVolume, bubblePt, fixTime=60*60, fixes=3, fixVolume=2

Example:
esp>&nbsp;&nbsp;&nbsp; startTube 3&nbsp;&nbsp;&nbsp;&nbsp; #pull WCR puck from tube 3, discard into tube 2
esp>&nbsp;&nbsp;&nbsp; wcr&nbsp; 200, 24&nbsp;&nbsp;&nbsp; #sample 200ml, filter bubblePoint of 24psi
\#defaults to 3 (20 minute) fixes of 2ml each.

\[Short Sandwich Hybridization phase 2 for in lab testing\]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; shortSh2(signal=:sig1, hash={}, &wcrBlock)

Examples:
esp>&nbsp;&nbsp;&nbsp; startTube 2&nbsp;&nbsp;&nbsp;&nbsp; #pull pucks from tube 2, discard into tube 1
esp>&nbsp;&nbsp;&nbsp; shortSh2 :sig2, :assay=>:bac&nbsp; #run BAC assay using :sig2

esp>&nbsp;&nbsp;&nbsp; shortSh2(:sig1, :assay=>:hab)
{wcr 50, 24}
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #hab assay followed by wcr
\\

\[Harmful Algae Bloom\]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; HAB(sampleVolume=400, wcrVol=50, &cleanup)&nbsp;&nbsp; #with initialPurge
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; hab(sampleVolume=400, wcrVol=50, &cleanup)&nbsp;&nbsp; #w/o initialPurge

Examples:
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; startTube 7&nbsp;&nbsp;&nbsp;&nbsp; #pull 4 pucks from tube 7, discard into 6
esp>&nbsp;&nbsp;&nbsp; HAB&nbsp;&nbsp;&nbsp; #sample 400ml, wcr 50ml, standard killIntake cleanup
esp>&nbsp;&nbsp;&nbsp; HAB 1200, 100&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #1200ml sample, 100ml wcr
esp>&nbsp;&nbsp;&nbsp; hab(1000)
{endPurge}  #1000ml sample
                #skip intialPurge, do not purge or kill Intake


\[Larval\]
        LARV(sampleVolume=400, wcrVol=50, &cleanup)   #with initialPurge
        larv(sampleVolume=400, wcrVol=50, &cleanup)   #skip initialPurge

Examples:
esp>    startTube 7     #pull 4 pucks from tube 7, discard into 6
esp>    LARV    #sample 400ml, wcr 50ml, standard killIntake cleanup
esp>    LARV 1200, 400         #1200ml sample, 400ml wcr
esp>    larv(1000) {endPurge}
&nbsp; #1000ml sample
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #skip intialPurge, do not purge or kill Intake
\\

\[Bacterial\]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; BAC(sampleVolume=100, wcrVol=50, &cleanup)&nbsp;&nbsp; #with initialPurge
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; bac(sampleVolume=100, &cleanup)&nbsp;&nbsp; #without initialPurge

Examples:
esp>&nbsp;&nbsp;&nbsp; startTube 5&nbsp;&nbsp;&nbsp;&nbsp; #pull 4 pucks from tube 5, discard into 4
esp>&nbsp;&nbsp;&nbsp; BAC&nbsp;&nbsp;&nbsp; #sample 100ml, wcr 50ml, standard killIntake cleanup
esp>&nbsp;&nbsp;&nbsp; HAB 1700, 800&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #1700ml sample, 800ml wcr
esp>&nbsp;&nbsp;&nbsp; bac(1500, 500)
{endPurge}
&nbsp; #1500ml sample, 500ml wcr
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #skip intialPurge, do not purge or kill Intake
\\

\[Demoic Acid\]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; DA(sampleVolume=750, &cleanup)&nbsp;&nbsp; #with initialPurge
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; da(sampleVolume=750, &cleanup)&nbsp;&nbsp; #without initialPurge

Examples:
esp>&nbsp;&nbsp;&nbsp; startTube 6&nbsp;&nbsp;&nbsp;&nbsp; #pull 3 pucks from tube 6, discard into 4
esp>&nbsp;&nbsp;&nbsp; DA&nbsp;&nbsp;&nbsp; #sample 100ml, NO WCR, standard killIntake cleanup
esp>&nbsp;&nbsp;&nbsp; DA 1200&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #1200ml sample, no wcr
esp>&nbsp;&nbsp;&nbsp; da(1250)
{\|ports\| endPurge(*ports)}  #1250ml sample, no wcr
                #skip intialPurge, do not purge or kill Intake


\[Harmful Algae Bloom plus Demoic Acid\]
        HABDA(sampleVolume=400,daVolume=750,&cleanup)  #w/initialPurge
        HABDA(sampleVolume=400,daVolume=750,&cleanup)  #w/o initialPurge

Examples:
esp>    startTube 4     #pull 7 pucks from tube 4, discard into 3
esp>    HABDA    #sample 400ml, wcr 50ml, DA 750ml,  standard cleanup
esp>    HABDA 500, 300      #sample 500ml, DA 300ml, standard cleanup
esp>    habda(1200, 500) {|ports| endPurge(*ports)}
)}
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #1200ml sample, 500ml DA, (50ml wcr)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #skip intialPurge, do not purge or kill Intake
\\

==============
Image Capture

All the above protocols (except wcr) take additional (optional)
:key=>:value type parameters that can be used to alter the image
capture settings.&nbsp; By default, three images are taken.

Image #1:&nbsp; 10 seconds with 4x4 binning
Image #2:&nbsp; 30 seconds with 4x4 binning
Image #3:&nbsp; hi-resolution Auto exposure

The :image key can be used to override this for a
given protocol run as follows:

esp>&nbsp;&nbsp;&nbsp; HAB 500, 50, :image=>\[5, :hires, 40, :auto, :midres, 20\]

This takes the following images:

Image #1:&nbsp; 5 seconds with default (4x4) binning
Image #2: 40 seconds with no binning (hi-resolution)
Image #3: hi-resolution Auto exposure
Image #4: 20 seoncds with 2x2 binning

See the Exposures, ImageMode and PuckCamera declarations in
shallow/configure.rb for more details on setting default
binning, image output directory, etc.

==============
Gigi's puck handling comands have undergone quite a bit of revision
over that past couple months.
Here's an updated command reference:

\*Puck Handling commands\*
\[This is copied from a mail I originally sent the list on 1/18/07\]

CC.loadPuck&nbsp; label, fromTube=nil
PC.loadPuck&nbsp; label, fromTube=nil
\# load a puck from the specified carousel tube into
\# the respective clamp (CC or PC).&nbsp; Use the required
\# puck label help to track it.&nbsp; Typical labels are:
\#&nbsp; :sh1, :sh2, :lyfil, :WCR, etc.&nbsp; The labels will soon enable
\# the ESP to produce instructions for loading
\# the carousel prior to a mission.&nbsp; For now, they
\# just show up as helpful comments in the log.
\# If the fromTube is not specified, then the puck
\# is taken from the currently defined "startTube"
\# If that "startTube" is empty, it advances
\# "startTube" to the next tube automatically.
\# This lets puck sets span tubes if desired.

CC.unloadPuck&nbsp; toTube=Storage.dstTube
PC.unloadPuck&nbsp; toTube=Storage.dstTube
\# unload puck in specified clamp to specified carousel tube.
\# If toTube is not specified, the puck is stored
\# in the "destination tube".&nbsp; For now, the "destination tube"
\# is simply one less than the current startTube.
\# For this reason, is it not advisible to set startTube to 1.

startTube&nbsp; tubeNumber=nil
\# define the current start or sourceTube for loadPuck.
\# if tubeNumber is omitted, the current startTube
\# is returned, unchanged.

dstTube
\# returns the current default destination tube for
\# unloadPuck.&nbsp; There is no way to set this explicitly.
\# For now, it is defined as 1 less than startTube.

access&nbsp; tubeNumber=SC.position.base
\# Rotate the carousel such that the specified tube
\# is accessible for manually loading and unloading pucks.
\# if tubeNumber is omitted, the currently selected
\# tube is made accessible.

CC.contains
PC.contains
\# return the label of the puck currently clamped
\# Handy if you've forgotten what's where...

Flush.to CC
Flush.to PC
CC.loadFlush
PC.loadFlush
\# all these simply load the flush puck into the specified clamp

Flush.garage clampledPos=nil
\# put the flush puck back into its garage
\# The clamp need not normally be specified, as the system
\# will track where the FlushPuck is currently clamped.
\# It may be specifed to explicity override the system's
\# record of the current FlushPucks position.

PC.unloadFlush
CC.unloadFlush
\# equivalent to
\#&nbsp; Flush.garage PC&nbsp; or&nbsp;&nbsp; Flush.garage&nbsp; CC

Puck.move&nbsp; fromTube, toTube
\# move the tube at the top of tube fromTube
\# to the top of top toTube

Puck.count&nbsp; tubes=1..SCtubes
\# count the number of pucks in the specified tubes
\# of tubes is omitted, count the # of pucks in all tubes.
\# This works by measuring the height of each respective
\# puck stack.

Storage.pucks
\# returns a hash of tube numbers to their respecive
\# puck stack heights.&nbsp; The unit of measure such that
\# 1.0 = one standard puck.&nbsp; The results are fractional
\# due to measurement errors and puck height variences.

Storage.pucks.sort.collect
{\|x\| x.last ? x.last.round : x.last}
\# This incantation will return an array with each element
\# corresponding to the number of pucks in that tube.
\\

=================

Multithreading has introduced the concept of locking the Arm and the
FlushPuck to a particular thread to ensure that no other thread can
hijack those resources while that are in use.&nbsp; The FlushPuck and Puck
load/unload commands handle this locking more or less transparently.
The Arm is locked for as long as it takes to complete the requested puck
move.&nbsp; The FlushPuck is locked whenever it is not garaged.

If a script attempts to move a puck while the Arm is locked, you will
see the message:

Waiting for (threadName) to free Arm
==or==
Waiting for (threadName) to free FlushPuck

Normally, the thread will eventually free the resource, allowing the waiting
thread to continue after claiming it.&nbsp; However,
The system can become confused if a puck movement is interrupted either
by an error or user abort.&nbsp; In this case, the thread that locked the Arm
and/or FlushPuck may be dead and the system in an indeterminate state.
The commands:

Arm.reset
FlushPuck.reset

May be used to in this case to reset the locks so that new threads may
access the resources.&nbsp; Normally, these command would be executed
only after the ESP was carefully inspected and returned to a safe state
using low level Arm.commands.&nbsp; For instance, if a user aborted loading
a FlushPuck into CC, the reovery sequence might be:

CC.open
Arm.releaseAt&nbsp; :garage
Arm.reset
FlushPuck.reset

Note that, if another thread is waiting on the resource, it will be able
to acquire it and continue after Arm/FlushPuck .reset.&nbsp; Therefore,
it is important not to reset until the system is put back into
a "safe" state.&nbsp; Also note that the primitive Arm.commands
do not respect the state of any locks, whereas the FlushPuck
and other higher-level puck movement commands do.
This rule allows users to interactively move the Arm to clear
errors without first resetting the locks.

And, a quicky new Arm command:

Arm.withdraw
\#retract the arm without opening the hand.]]></property>
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<property name="body"><![CDATA[Present: Chris S., Wayne, Chris P., Roman, Doug, Jim, Brent

Absent: Cheri, Scott

h3. Machine Builds

* NEO is ready for new lid.&nbsp; Needs bulkhead valves, brackets, and top of can fittings.&nbsp; Getting ready for pier deployment.&nbsp;
* Two of our radios need repair.&nbsp; Brent has RMO #s and will task Cheri with their return.

h3. MFB&nbsp;


h3. Drifter

* Jon Erickson's 2009 time on CMORE to design a 200m can is on-hold pending Gene's end-of-year review on drifter feasibility.

h3. Software


h3. Deep ESP/DWSM

* Doug's detective work found that the SS parts sitting in 2% bleach was causing rust, specifically crevice corrosion.&nbsp; Using more dilute bleach (0.2%) followed by water wash should be okay to the metal.

* We have a quote from FloTech for the Benthos ducer baffle.&nbsp; Will tell Hans told to order; charge $3600 to ASTEP II.

h3. GUI


h3. Deployment Issues

* &nbsp;Brent noticing hand jitter on both Moe (at M0) and Mack (at SC).&nbsp; Thinks its from belt tensioning changing and slower sampling rate of the firmware.&nbsp; These have slower 32hz sampling protocol in the firmware.&nbsp; Gordon has newer 64Hz, and tuning doesn't need to be so precise.
* Bruce's cable has been dissected, and it is thought the break in leads #1 and #2 occurred \~2 inches from the start of the bell termination housing on the bailer end of the EM cable.&nbsp; Jim Scholfield thinks he can get it re-terminated with the remaining EM cable to be ready next Thursday.&nbsp; This changes our plans for Bruce, which we will now try and 're'-deploy on Monday or Tuesday (Oct 12/13).&nbsp; Will check with Grech about which will work for DMO; maybe go with Shana Rae if needed.&nbsp; Roman will dunk radio-box looking for leak.
* D-ESP.&nbsp; After plugging in, hand seemed to jam a puck at top of stack #2.&nbsp; Brent and Scott seemed to fix it--it's now run 3 shuffle puck routines, and Brent has pumped water through the core.&nbsp; Mission will begin tonight.&nbsp; Ideas for figuring out why it did this was to cold-shock it in the van, and use dial indicators to see how much physical change cold actually induces.
* Brent noticed that when turning off power to DWSM, the compensating temp gauges in the new pressure sensors cool down, so when powered again, there is all sorts of funkiness while they re-warm.&nbsp; Decision is to leave Gordon on all the time.
* Chris P. published Gordon's mission [here(v4)|^GordonVer4ScheduleOct09.pdf].

* SC pier deployment.&nbsp; Pumps are both in Bldg B lab near the eyewash.&nbsp; Brent and Jim will go to Pier Weds to work on setting up communications.&nbsp; Meet with city officials next Weds about using their network to communicate with our system.
\\

h3. &nbsp;Other Items

* For those listed on the R&D 100 award, there will be a ESP TEAM PHOTO on Monday.&nbsp; Time still to be set-up with Todd.&nbsp; Stay tuned.
* There is a new listserv for discussion of ESP problems and technical issues:&nbsp; ESPTECH.&nbsp; Please use that when discussing difficulties.&nbsp; Dirty laundry, even if about to be cleaned, still stinks...]]></property>
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<property name="body"><![CDATA[h2. Overview

h2. Notes

The printer used by [~scholin] is a custom printer. It can not output GAL files. It does put out a text file that I'm trying to parse and work with. A copy of the file is checked into [SVN|http://kahuna.shore.mbari.org/viewvc.cgi/esp/trunk/esp-imaging/src/test/resources/imaging/2_22_08comptest_2008-02-25_142348_Run.txt?view=markup].

h3. Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:
{noformat}
SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK
{noformat}

_SpotX_ and _SpotY_ are coordinates in micrometers starting in the upper left hand corner of the paper. The _0, 0_ point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out.

_SrcWell_ indicates the contents of the spots. For example, all spots from the _C-1_ source well will have identical chemistries applied.

h3. Image Analysis

Maximum Entropy thresholding does a decent job of delineating the control spots. Unfortunately, I haven't found a technique for delineating the spots that don't go off. In fact those spots can contain values within the range of the background noise. 

{gallery}

h4. Possible avenues of exploration

The ESP folks would like an automated image analysis package that:
# Reads the image
# locates the spots (either with or without the help of the GAL-like file)
# Read the highest 8x8 block (full size image) or 4x4 block (half-size image) average within the spot. The block average is square with no weighting applied.
# Return a text file (Tab or comma delimited) with:
#* Average intensity associated with the _SrcWell_ (i.e. C-1, A-1, etc.)
#* Standard deviation by _SrcWell_
#* Average intensity of background disk (excluding spot values)

h4. Analysis Steps (in progress)
# Read in _layout description file_ with LayoutViewer
# Generate a _single assay_ image.
# Select the control spots and export spot list to a new _Layout Description File_
# Read in single control spot list
# Read in measurement image.
#* Convert to binary image using _maximum entropy threshold_ technique
# Convert both images to polar and log-polar coordinates
# Calculate translation and rotation of control spots using techniques described in [Robust Image Registration Using Lo-Polar Transform|https://alfresco.mbari.org/alfresco/webdav/Projects/900612_2G_ESP_Applications/Docs/Array%20Imaging%20Docs/Robust%20Image%20Registration%20Using%20Log-Polar%20Transform.pdf]



h3. References
# Old ESP Matlab toolbox at [http://moonjelly/cgi-bin/cvsweb.cgi/ESP/matlab/]
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<property name="body"><![CDATA[h2. Lessons Learned meeting after September 2011 Drifter Cruise to Station Aloha, Hawaii


* Shipping van fan velocity needs to be turned down if we are to work inside.  Noise is not too bad, but air velocity stirs up lots of dust.
* Van left MBARI Aug 17, arrived Hawaii Aug 25.  KM deployed Sep 6.  This was barely enough time to get everything ready.  In future, when running PCR, we need {color:#ff0000}3 weeks minimum{color} to prepare.
* MFB preparations.  We should get it ready, but once arrived, do full runs and spot-compare to pre-shipping.
* Must have extra tools here at home, so traveling group does not clean us out.
* Rigging box spares in case we deploy back home at same time.
* This deployment (Sep 7-17) used 1400 minutes of Iridium air time.  Was slow and dropped frequently.  Seas were calm so no need for constant engineering data to be transferred.
** Was discussion of how to compress files to more efficiently send via Iridium.  Perhaps .JPG conversion of TIFF's?
* Retrieved NO DATA from the PAR sensor.  PAR log says it rec'd a ctrl-C character, which stopped data logging.  Perhaps happened when ESP re-powered?  We need either NO comms to PAR so it's always running, or TOTAL comms, so we can query it and restart if necessary.
* Important to time-sync all ADCP's with the ship.

Many other engineering issues learned are in this document:
# [Lessons Learned from CMORE Hawaii cruise (Sept 2011)|^Lessons Learned.docx|Lessons Learned]]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Birch, Everlove, Jensen, Pargett, Harris, Roman, Gomes

h3. Tech Transfer

Cheri update on Bruce.&nbsp; Needs to install hand before moving on.&nbsp; Brent would like access to work on race-ramming routine.&nbsp; He will finish Friday; Cheri gets Bruce Monday.

&nbsp;Mack running smoothly.&nbsp; Will run HAB/DA tomorrow (Friday) and continue box mission


h3. MFB

Unable to duplicate the positive amplification we got last week for the Moore report.&nbsp; Addie to check the thermal profile.


h3. Software

Brent has a variety of software issues to work on, but most effort is focused on keeping Mack running smoothly


h3. Sphere and 4K DWSMS

Pumps continue to arrive.&nbsp; Two additional surface cans have various manufacturing defects.&nbsp; Doug working with Mike Parker to determine which pieces get sent back.


h3. GUI Development

Not discussed

Deployment issues discussed.&nbsp; We have asked and been granted permission to stage ESP in Bldg D.&nbsp; Discussion ensued about our reputation before and after deployments, and whether we should have a dedicated support person to help pre and post-deployment activities proceed smoothly.&nbsp; We will ask Mark B. if Jim Scholfield might be that person.&nbsp; Must check with Chris S. about having resources to use him.]]></property>
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https://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/Gen2%20MFB%20manual/

There are two PDF Versions: [1.0.4|https://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/Gen2%20MFB%20manual/MFB%20User%20Manual%20v1.0.4.pdf] or [1.0.81|https://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/Gen2%20MFB%20manual/MFB%20User%20Manual%20v1.0.81.pdf]
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<property name="body"><![CDATA[Present: Doug P, Addie, Chris S, Cheri, Brent, Scott, Kevin G, Jim, Visitor-Jack Regan

h3. Tech Transfer

* Mack running well so far.  One week down\!
* We will try and keep the late May dates for pickup and dual deployment.  May 27 Pickup Mack, May 28 Deploy Bruce & Neo.  As dates approach, we'll decide on two teams; one team to ready two instruments, one for Mack pickup.
* Bruce:
** Temperature calibration on Monday after a weekend cool-down
** middle of week do roman flush
** end of week science gets it
* &nbsp;Cheri brought in reps from slider manufacturer.&nbsp; They have a model in which the races do not drift, but some parts of plastic.&nbsp; Unknown how this will respond to vapor environment in can.&nbsp; They left one slider, will send another, and we will begin temp and EtOH testing.
* Scott has prices on ordering/populating/building more dwarf and sleepy boards.&nbsp; Prices are as follows:
** Core: each needs 5 dwarves, 1 sleepy.&nbsp; Cost $7K for all components and wiring harnesses
** MFB: each needs 2 dwarves.&nbsp; Cost $2K for all components and wiring.
** This is what we decided we needed:
*** Dwarf boards:
**** Moe&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 6
**** CMORE&nbsp;&nbsp; 6
**** MFB&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 14
**** DWSM&nbsp;&nbsp;&nbsp;&nbsp; 6
**** Spares&nbsp;&nbsp;&nbsp; 10
*** 4 Sleepy boards

h3. MFB

* AIV hole sizes.&nbsp; It has been decided that we will order 10 custom AIV's, each with four 1/4-20 ports and two 10-32 ports.&nbsp; Rotors with custom grooves will have the 'larger' grooves to accommodate the 1/4-20 hole sizes.&nbsp; Addie will add DWSM components to any order she needs to place.
* Addie has found that the encoders we've been ordering are no longer made.&nbsp; Another manufacturer need be found.&nbsp; Group thinks this will not be difficult.
* Other things to order for big build:
** SPE columns
** motor gearing
** motor coupler
* SPE heater still needs some design work.&nbsp; Then must do cold testing.

h3. Software

* Low power boards.&nbsp; Decided that low power, long-term deployments were not on the schedule for the next 1\+ years, so resources will be redirected to other areas (e.g., a robust core).&nbsp; Brent had suggestions on things we could continue to look into to lower our power draw (power down battery, slow the CPU, change our intake/out-take hardware).&nbsp;
* Cheri found bug in puck counting when there was an arm miscalibration.&nbsp; Fix to be tested on Bruce.
* Brent working on implementing on Bruce e-mail notification of problems
* Working on modification fo firmware for DWSM.

h3. Sphere and 4K DWSMS

* Surface cans from IMT Precision.&nbsp;
** Cans have been 'repaired' and will arrive next week
** Scott to order lid connectors
** Doug to order lid plugs for pressure testing
** we will test with He and test tank
** Although out of spec, we will take one set of top/bottom lids.&nbsp; These to be tested&nbsp; once plugs arrive next week.
** lids to be moved to tin shed for storage until ready for use
* Doug to hold new DWSM design review in 2-3 weeks.

h3. GUI Development

* Kevin to meet with Brent to discuss issues related to mission scripting.]]></property>
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<property name="body"><![CDATA[Meeting called by Chris Melancon of Spyglass to discuss LLNL tech transfer isses.

&nbsp;Attendance:

John Dzenitis (LLNL)

Dean Hadley (LLNL)

Bill Bennett (LLNL)

Ivory Engstrom (McLane)

Chris Melancon (Spyglass)

Jim Birch (MBARI)\\

Much discussion about issues with manufacture of the modules.&nbsp; Ivory arrived with a well-organized list of questions related to manufacture and production of PCR-modules.&nbsp; I learned that of the 12 modules MBARI has purchased, they are divided into 2 lots.&nbsp; First lot does NOT have pins holding end-plates into the cover; second lot does have these pins.&nbsp; There is also a newer version of the firmware that we could have Vincent burn.&nbsp; This would require removing all our boards, sending to LLNL, he would burn and return. ]]></property>
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<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.

June 26 - continues to run, but lost internet access due to an unknown networking error.

h3. {color:#ff00ff}Diversion Experiment; So. California Deployment of ESP-Gordon / NEO{color}

Aug 30 \-\- Haul instrument and gear in trailer and MBARI van to deploy on OCSD R/V Nerissa.  Calm seas, hot weather, instrument in \~10:30am.  Gordon w/PCR, CTD, ISUS, cell-phone modem (T-Mobile).  Sewage diversion to begin Sep 11, 2012. Machine located at 33.59703 \-117.94623.&nbsp; Divers from Orange County Sheriff's dept.

Kevan collecting data here: [http://www.stanford.edu/~kevany/ESP/].

Sep 14-noticed CTD battery draining faster than expected because of optode.&nbsp; Also, ATV encoder in MFB&nbsp; kept returning 511, which is 2**9-1&nbsp; meaning all bits are stuck high--typical way they fail.&nbsp; Stopped PCR, continued SHA, but with dead CTD no contextual data to adaptive sample off of.&nbsp; Decision to flip for NEO on Sep 26.

Sep 26-recovered ESP-Gordon and swapped both batteries and ESP-Neo.&nbsp; Also changed CTD so now no optode (O2) measurments.&nbsp; One power cable fizzed away.&nbsp; Connector on pickle jar loose.&nbsp; But NEO now running well. Skipper gave deployment coordinates of 33 35.829 &nbsp; \-117 56.759.&nbsp; Xeos says&nbsp; 33.59702 \-117.94604.&nbsp; Water depth 18m.&nbsp; CTD/can depth=6.3m.&nbsp; Divers from LBAoP--Eric Castillo and Steve Lang.

Oct 16-Recovered ESP-Neo.&nbsp; Divers from LBAoP--Steve Lang and Veronica Anderson.

h3. {color:#ff00ff}Fall CANON--Drifter with ESP-Moe / Moe{color}

WF leaves MBARI Sept 10.&nbsp; Moe with PCR, ISUS, CTD, PAR, and buoy has downward ADCP.&nbsp; Roman and Julie R. on ship.

Moe went into water Sep 11. First phase slated for 6pm.

Pulled Sep 17 (10:30am).&nbsp; E/M cable started flaking out either due to connector or bad ethernet extender.&nbsp; Decision to end mission unrelated to this. ]]></property>
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<property name="body"><![CDATA[Present: Cheri,  Doug, Brent, Jim, Scott, Chris S., Chris P., Roman

This meeting was called mainly to discuss:
# Gordon repairs
# Schedule up to the next MARS deployment (14Dec2009)
# Adding o-ring groove on collection clamp
# Steve Hallim visit Monday

h3. Machine Builds


h3. MFB&nbsp;


h3. Drifter


h3. Software


h3. Deep ESP/DWSM

* &nbsp;Looks like all errors on the first MARS deployment were due to a loose set screw on the motor gear that rotated the carousel.&nbsp; This is easily repaired, and there was much discussion on how to fix in the future.&nbsp; Immediate solution (short of welding gear onto motor shaft) is to machine larger slot in base to allow movement testing of gear tightness, and calibrate hand and carousel from both directions.
* New temp sensor has pigtails and now has been dipped in conformal coating for x-tra protection.&nbsp; We should test to see how well coating works.
* O-Ring groove.&nbsp; We will NOT do it for Gordon, but begin the design/machining/testing process, using Betty.&nbsp; We will calibrate her first without the mod, then after the 14th deployment add the change and compare calibration numbers.

h3. GUI


h3. Deployment Issues

* Calendar for upcoming MARS deployment hammered out with Science. Rough sketch hanging on fume hood in Scholin lab.

h3. &nbsp;Other Items

* Steve Hallim from the VENUS project (Canada) is arriving Monday to discuss possible placement of ESP on their cable system. ]]></property>
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<property name="body"><![CDATA[h1. Concept of Operations for Cawthron Deployment.

{color:#cc0000}{*}As of Jan 5, 2012:*{color}

h4. Where?

Tasman Bay east of Riwaka

CAWTHRON INSTITUTE
98 Halifax Street East Nelson 7010
Private Bag 2 Nelson 7042 . NEW ZEALAND
Tel \+64 3 548 2319
Fax + 64 3 546 9464
www.cawthron.org.nz

h4. When?

Looking at a 30-day deployment in the April/May 2012 time frame.  They want to deploy when there is a high likelihood of rain.

h4. Targets?

This is from Oct 28, 2011 email from Chris Cornelisen:
{panel}It would be best to focus on water quality/HAB; however, we are also are interested in running the larvae array; hence we would likely split samples as suggested in Kevan's earlier email (e.g. 21 QPCR/HAB + 7 LARV, total 28 samples), with the remaining samples archived.  Runing the GenBac marker instead of one of the Pseudo ones would also be good. I'm not convinced of the usefulness of the HBac marker at this stage. We can do bench top work and test the markers/arrays ahead of time using samples from the site and your protocols.  Kevan/Chris P - feel free to contact Kirsty Smith directly to further discuss next steps. {panel}

And items related to sampling design:
{panel} Prior to deciding on whether we would use an environmental trigger(s) for sampling, We'd like to put together a wider plan for the deployment of the ESP. i.e. how will the ESP contribute to the bigger picture and augment additional efforts (Synoptic surveys, additional buoys/sensors, etc.)?  Basically, we would aim to deploy it within a broader temporal and spatial framework as used in the recent Ryan et al. paper (albeit with less toys). I'll draw up a straw man for this.{panel}

h4.  Communications?

Brent has communicated with Paul Barter and we will be using a cell-phone modem to connect buoy to cell-phone network in/near Nelson.

h4.  Shipping?
Two cores (both with MFB modules) will be shipped to NZ: Gordon and Neo.
These will be 'dry shipped' via air freight, either in their pressure housings or in (still-to-be-built) plastic boxes, which will make customs easier to navigate.
Cawthron will order all reagents from manufacturers; MBARI will thus avoid Customs issues.
Printed arrays will be (air?) shipped separately.  Must research restrictions for flying nitro-cellulose.

Buoy and mooring infrastructure will travel via boat to NZ.

h4.  Who and how long?

TBD]]></property>
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<property name="body"><![CDATA[Mooring configuration:
2 dry battery packs
1 CTD
no ISUS
1 MaCK with MFB and some reagents
1 Mooring base

ESP in Air Weight: 680 lb
ESP and Anchor in Air : 1156 lb

ESP in air Anchor in water: 1092
ESP and Anchor in water: 202 lb

Anchor weight in water = 1092 - 680 = 412 lb

ESP bouyance = 202lb - 680 - 412 = -890 lb

Total Bouyance = 680 - 890 = 210 lb

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<property name="body"><![CDATA[# The user cannot change the make up of a phase once it has been defined.  If the sequence or timing of the contents of a phase changes, a new phase must be created.
# The combination of the phase identifier and the protocol identifier is a "unique key" in determining how much of the various consumables will be used.
# The phases will have worst case times associated with them where they could run up to, but never over, that amount of time.  The default worst case is 4 hours, but some (like HABDA) could go to 6 hours.
# The amount of waste storage available and the number of pucks are the main limiting factors.]]></property>
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<property name="body"><![CDATA[# Do we need to track the serial numbers of the pucks in the application?
# If we print barcodes on filters, do we want to track in the application?
# Does the delay (7 minutes) only happen at the beginning of each phase or each protocol?
# Is max duration at the phase level or protocol level?
# What sort of things go in Event_Types?  I think we are using those for mostly stuff that gets parsed out of the log file and stuffed into events, but should we have Protocol_Run, Phases, or Deployments in the event types even though they are actually subclasses?
# I think the Eventt hierarchy should look like Deployment->Phases->Protocol_Runs.  Just want to verify.]]></property>
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<property name="body"><![CDATA[This page lists some terminology and their definitions and context as they were used in the design work of the GUI application.  This is to ensure that when discussions are occurring, we are all talking about the same thing.
||Term||Definition||
| +*Sample Volume*+ | A volume of water that is drawn into the instrument that contains the organisms which the instrument is attempting to identify. The volume of water is never actually stored in the instrument, it is run directly through a puck and filter and then sent back out to the environment. |
| +*Probe Array*+ | |
| +*Filter*+ | Special paper that is used to filter out suspended material from a water sample. Sometimes the filter has probe arrays printed on it, but not always (for example, WCR has no probes as it just archives the organisms). |
| +*GAL File*+ | File that is produced by the filter printer and contains the locations in X,Y coordinates and what probe arrays are at those X,Y coordinates. |
| +*Puck*+ | Metal ring that holds filter paper which is used to capture and process organisms. There are three types of pucks:
# Standard Volume Sample puck (SVS)
# High Volume Sample puck (HVS)
# Whole Cell Archive (WCR) |
| +*Collection Stage*+ | The location where a puck is loaded during sample collection. |
| +*Carousel*+ | Rotating set of tubes where pucks are stored. |
| +*Manipulator*+ | The mechanism which is used to move pucks to the various locations in the ESP. |
| +*Lysate*+ | A solution that is created by adding a solvent to the material that is filtered out of the sample water by the filter.  This solution is then used as the source for analysis.  Note the lysate can be split amongst many protocol runs (and other events). |
| +*Protocol*+ | This is a sequence of steps that are taken to perform some biological analysis. This is sometimes called an Assay. |
| +*Protocol Run*+ | This is the actual execution of a defined protocol. |
| +*Phase*+ | Consists of a cycle of instrument power up, a sequence of one or more protocol runs, and a power down.  Examples of phases are HAB, BAC, LARV, etc.  The concept of a phase is important as a mission script is defined using phases.  Phases can contain protocol run sequences that will take more than one sample of water. i.e. The relationship between phase and sample is one-to-many. Note also that the ESP normally goes into a low power, or quiescent, state. |
| +*Inital Purge*+ | When a phase begins, the ESP powers up and initializes itself.  If disinfectant solution was used in the previous phase, it will need to be purged by running a step called +*Initial Purge*+. |
| +*Mission*+ | This is a logical span of time in which an ESP instrument is operating which has some start and end time.  It is usually associated with a deployment and recovery of an ESP and consists of a sequence of phases separated by quiescent states. |
| +*Deployment*+ | Is used synonymously with *Mission* |
| +*Mission Script*+ | An ASCII file that contains Ruby commands that tell the ESP what actions to take at what times. |
| +*SHA*+ | Acronym for Sandwich Hybridization Assay |
| +*Standard Curve*+ | A curve that maps intensity to density of organisms.  You use it to take the intensity of an image and calculate the density of organisms in the sample. |
| +*Consumable*+ | Is any resource on the instrument that can be consumed.  Examples are:
# Power
# Reagants
# Capacities like waste (there are 2)|

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<property name="body"><![CDATA[Present: Cheri,  Doug, Brent, Jim

Absent:&nbsp; Chris S., Scott

h3. Machine Builds

* Scott provided rough [board prices|^McLane Cost Estimate.xls|Core Board Costs].&nbsp; Numbers and invoice sent to Mike Pinto to bill McLane.&nbsp; Money to be returned to 900915.
* Most recent drawings for screens are here--> [SH1 screen|^SH1 Frit drawing revB.pdf|SH1 screen drawing] and [WCR screen|^WCR dispersion Screen drawing revA.pdf|WCR screen drawing].

h3. MFB&nbsp;


h3. Drifter


h3. Software

* Both Moe and Bruce have thrown errors on the processing side where valve/syringe loses it's position.&nbsp; Brent doesn't think it's mechanical but rather a timing issue between the firmware and the FPGA. &nbsp; Gordon shows no problem but is running the newest firmware
* Must find out what version of CPLD code and firmware is on each machine.

h3. Deep ESP/DWSM

* Weathered out of the Oct 13 pickup of Gordon (D-ESP).&nbsp; Next available Lobos day is Oct 27.

h3. GUI


h3. Deployment Issues

* Radio at Abes and at Brents are getting flakey due to introduced water.&nbsp; We will try butyl rubber tape to get us through this networked deployment.&nbsp; Boxes should be made for future deployments.

h3. &nbsp;Other Items

* Pier deployment
*** Brent measuring and ordering 2 boxes to contain electronics (and radio).&nbsp; should be in mid-next week
*** Brent and Doug checking out Pier tomorrow; where to mount things and water height at low tide.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Birch, Everlove, Jensen, Pargett, Gomes, Scholin

h3. Mack Deployment begins April 3

\\

Mack out of cold, and getting new lid.
Science still to drain waste and add new flush

Will perform 2 runs tomorrow (Friday).&nbsp; A pre-can DA (short) to confirm reagents work, then a full DA.

Monday will load pucks and can it.
Tuesday mount to mooring.
\\

Divers \-\- Mike Conway, Jason Felton

Crew \-\- Roman, Scott, Doug, Cheri, Jim

Discussion ensued about our can situation.&nbsp; We have two cans (a good one, and a stitch-welded one) and there was talk on logistics for this 2.5 month network deployment.&nbsp;

[Current schedule|ESPAPP:2008 Q1-Q2 Schedule (rev 6)] is

&nbsp;Deployment 1 is April 3-21 (Mack delivered on Shanna Rae, retrieved by Zephyr).&nbsp;
&nbsp;Deployment 2 is May1-27 (Mack delivered and retrieved by Zephyr).
&nbsp;Deployment 3 will be 2 ESPs (M0 and off SC) May 28-June 30 (Neo and a refitted Bruce via Zephyr)
&nbsp;]]></property>
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<property name="body"><![CDATA[Present: Cheri,  Doug, Brent (phone), Jim, Scott, Chris S., Chris P., Roman


h3. Machine Builds

* Betty finished and ready for science checkout.

h3. MFB&nbsp;


h3. Drifter


h3. Software


h3. Deep ESP/DWSM

* Deep recovery is next Tuesday, Oct 27.&nbsp; Doug will be only one going on Lobos.&nbsp; Once back in high-bay, will connect ethernet and empty \~15L of water from DWSM bags.&nbsp; Also bringing back Niskines (4L) with MARS water.&nbsp; Chris P., will be around for processing.
* Wednesday we'll crack the ball, remove Gordon and take to assembly lab, and let Brent play with puck handling to try and recreate error we saw.&nbsp; DWSM will go to the van.&nbsp; That evening or the next day Chris P. will remove WCR pucks for processing.

h3. GUI


h3. Deployment Issues

* Surface recovery.&nbsp; Slated for Weds/Thurs next week (Oct 28/29), will get 2 machines Weds, 1 Thursday.&nbsp; Paul Ban is 1 diver; need 1 more.
* Gene has need for a surface can; can get one Friday, but a lid issue.&nbsp; We'll see which can be spared.
* Chris S. mentioned checking Wattlo's to calculate total power consumption while out
* All cans will end in High-Bay where we'll run post-deployment negatives.&nbsp; John's been notified.&nbsp;

h3. &nbsp;Other Items

* Pier deployment
** Post-can QC of NEO got started late, so will not head to Pier until 12:30.&nbsp; Doug to drive instrument in van.&nbsp; Roman, Chris P & S, Scott going, will meet Brent.&nbsp; We should be running this afternoon.

* Ivory Engstrom visiting from McLane next Weds (10-28)
** McLanes building of a core is bringing many issues to the fore;
**** Camera: USB2.0 vs1.0.&nbsp; We will develop a controller to stand b/w camera and host
**** Various other issues will be discussed Weds with him.

* Harbans Dhadwal visit
** Arrives Friday; we will have MFB8 ready for him, but also MFB2 as a 'demo' unit.

* 2010 Zephyr schedule
** We have 7 Zephyr days sprinkled April \-\- Nov.&nbsp; All look okay except for last; Chris will try and get Nov 18 moved to Nov 1.

* Marcia goodbye part is Thursday Oct 29; Chris needs to attend.&nbsp; Jim will be at LLNL for McLane/LLNL/Spyglass mtg.]]></property>
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<property name="body"><![CDATA[h3. Outline of instrument plan for Jan-Jun, 2008

# One _week_ cold test of Mack w/ his new valves/hand starting Mar 17.
# Once Mack finished with box test, we replace with Bruce for box test.
# {color:#ff0000}{*}Deploy{*}{color} MACK (April 3-Shana Rae)
## {color:#0000ff}{*}Recover{*}{color} MACK Apr 21,&nbsp;-\- Shana Rae
# &nbsp;{color:#ff0000}{*}Deploy{*}{color} MACK (May 1 \-\- Zephyr)
# {color:#0000ff}{*}Recover{*}{color} MACK (May 27), {color:#ff0000}{*}Deploy{*}{color} *both* BRUCE and NEO (May 28 \-\- Zephyr)
# End mission Jun 30.

(ed. Mar 27, 2008)]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}3G Koa on AKU in Monterey Bay{color}


h6. *Jan 24, 2018*

Deploy Aku with Koa and 60 cartridge archival mission.&nbsp; Collecting \~32 samples for Ed and Kevan (eDNA), then running remainder (~19) as engineering tests with 20 minute filtering time-outs.

h4. {color:#ff00cc}Hawaii MiVEGAS cruise on R/V Falkor{color}

Three ESP instruments delivered:&nbsp; ESP-Koa, MV1, MV2

Three LRAUV were delivered:&nbsp; Opah, Aku, Ahi

They were paired as
Opah-no ESP (just CTD instruments)---during both legs, Opah flew recon in loops around sampling instrument (or tried to).
Aku / Koa
Ahi / MV1
MV2 was installed on bench in Falkor lab

*Leg 1:&nbsp; March 10-22, 2018*

Ahi/MV1 was first to launch (Mar 11), and was pulled under ship and damaged.&nbsp; Recovered \~2 hours later.

Launched Aku/Koa. sampled Mar 17-Mar21.&nbsp; Collected 38 field samples - of those 1 failed - leaked, 1 smeared.

&nbsp;*Leg 2:&nbsp; March 27-Apr 10*

Aku/Koa used again. sampled Mar 28-Apr2.&nbsp; Collected 56 field samples--of those 8 leaked (no sample), 1 smear.

h4. {color:#ff00cc}2G on Yellowstone River{color}

Deployed the following on *July 25, 2018* for full carousel of archives:

ESP-Gordon \-\- Livingston (Carter's Bridge).  45.597148, \-110.566021

ESP-Waldo \-\- Corwin Springs. 45.111612, \-110.793943

&nbsp;Recovered both instruments *Sept 5*.

h4. {color:#ff00cc}3G shakedown in MB for L. Erie{color}

*Aug 2-6, 2018*

First multicartridge L&G flight with SPR in MB.

h4. {color:#ff00cc}3G in L. Erie{color}

*Aug 20-Sept 4, 2018*

We arrived and started building instrument Aug 20.&nbsp; Sent in water Aug 23.&nbsp; Recovered Aug 26 and redeployed 27th.&nbsp; Ran Makai with Koa and 14 L&G cartridges and SPR module; remainder were archival.

h4. {color:#ff00cc}3G Tacklebox in Teton Valley{color}

*Sep 10-12, 2018*

Collected 5 samples (Flat Creek, confluence of Cache/Flat crk, South Park Flat Creek, Fish creek, pond on South Park Flat Creek).&nbsp; tested in situ for E. coli.&nbsp; 3 positives (but Ct's were 36-38, so low copy numbers).
\\
Collected hand sample along with 3G ESP sample.&nbsp; Used the Freedom 4 PCR module, hand-feeding it lysate created from our L&G cartridges.
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<property name="body"><![CDATA[Back to basics ...

# What does the ESP do?
## Collects discrete water samples
## Concentrates microorganisms or particles
## Automates application of molecular probes which identify microorganisms and their gene products
## Archives samples for later analysis]]></property>
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<property name="body"><![CDATA[Present: Scott, Doug, Chris S., Jim, Wayne, Brent, Kevin
Absent: Cheri (SolidWorks training), Addie (maternity)

h3.


h3. Machine Builds

* &nbsp;o-ring test out.&nbsp; No results yet.&nbsp; O-ring in Mack was not sealing properly; needs exploring/explanation.
* Pucks.&nbsp; Have one set left to be etched, which will give us 4 complete snap-puck sets; all same rev, but different lots.

h3. MFB

* Getting close to the end of the 2-grill build.&nbsp; 1 has had fluidics checked out; both have syringe and heaters calibrated
* Chris P running dye test on MFB01 now, may try and run PCR tomorrow
* Tomorrow AM will meet with McLane and map out the concepts of a visit for the core build.

h3. Software

* &nbsp;Moving from development mode to more a manufacturing mode has caused Brent to re-jigger the config files on both the Core and MFB's.&nbsp; Each now has a PreConfig.RB, Config.RB, and PostConfig.RB, with the pre\- and post\- common to ALL MFB's; the Config.RB is unique to each unit.&nbsp; This change is also being implemented on the cores.
* Brent has discovered a file accessing issue with the CTD that will require Bob Herlien's help for a week in early 2009.&nbsp; This should stop the hiccup we've seen when hooking up new CTD's to the core(s).
* Xylinx issue still causing heartburn.&nbsp; Now using old code, with both old or new compilers, produces corrupted results.&nbsp; It has worked for many years, but now is flaking on us.&nbsp; Wayne to delve into what is going on--this is top priority since DWSM uses these same xylinx boards for quadrature decoding.

h3. DWSM


h6. +Sphere+

* Chris S. has found that near-term 2500m is max depth we may want to go.&nbsp; He has found that depth certification is very strict if Alvin will be near it (test at 150% 10x then hold 1hr at max).&nbsp; Much discussion on whether this is necessary, what would we need Alvin for, the need for a manual release.&nbsp; We want to go to maximum depth, but don't want the setup to become an engineering project in itself.
* DECISION:&nbsp; we will outfit w/ strain guages and go to maximum (either of the test facility or to 3750m)
* Will get quotes from both Southwest and Port Heuneme;&nbsp; Will try and have tested in January.

h6. +Elevator+

* Have learned that prime real estate near MARS has already been taken, so we will need some type of long or extension cable, which may impact elevator design.
* CDR will be Wednesday (December 17).&nbsp; Jim will schedule

*{+}DWSM{+}*
* No work since last week.

h3. GUI Development

* &nbsp;Kevin has taught Roman M. how to download data, which he has done for the last triple-deployemnt.

h3. Other Items:

* &nbsp;Discussed potential classes at JALA for Brent and Scott. Both will be going, with perhaps 2 science people.&nbsp; Must get logistics to Cindy by tomorrow.
* Chris has spoken to Grech about moving ship days and not looking good.&nbsp; Solution will be to move Feb and Aug orphan days to the Fall for another MARS hookup.&nbsp; Although no extended running time before Flyer cruise in June, his deemed acceptable. Dates now look like this:
*** Dive 1:&nbsp; March 25--no core but elevator, DWSM, sphere
*** Dive 2:&nbsp; April 7-core in sphere, elevator, DWSM-run WCR
*** Dive 3:&nbsp; April 14-core in sphere, elevator, DWSM-minimal chemistry (SHA)
*** JUNE 8-12--Flyer cruise (these dates may be moved a few days earlier, depending on DMO scheduling changes)
*** AUG 16-26--Flyer to Axial
*** Dive 4:&nbsp; Fall #1 \-plug into MARS (date depends on what we can get that first week)
*** Dive 5:&nbsp; Fall&nbsp; #2\- pick up from MARS
*** Dive 6: Nov 4--plug into MARS, pickup in early 2010]]></property>
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<property name="body"><![CDATA[Present: Scott, Doug, Chris S., Jim, Addie, Brent
Absent: Wayne, Cheri, Kevin

h3.


h3. Machine Builds

* &nbsp;Allison replaced Mack o-rings with silicone (red ones); Roman doing dunk test in various reagents.
* Procedure when 'getting' any boards is to notifiy Dick Littlefield, who is the inventory keeper.&nbsp; Addie to let him know of the boards she borrowed from Wayne.

h3. MFB

* Addie has rec'd doctors instructions for bed rest until she has her baby, thus will not be returning to the lab after today.&nbsp; We will continue with the McLane visit using Cheri and Scott.
* Addie will change the stator and install Scott's taffy pull mixing tube on MFB1 so we may run PCR next week when Kendra comes to visit (Friday).
* We will order 9 regular 14-port stators
* First grill is called MFB1, MFB2 & MFB3 will be built with McLane.&nbsp; The MFB on the tombstone is called either 'MFBNeo' or 'the tombstone'.

h3. Software

* &nbsp;Garbage clean-up fix seems to have worked.&nbsp;
* Brent working on multiple config-file issues regarding linking MFB to a core
* Must make sure back-plane and grills are labeled, so&nbsp; config files stay linked to the appropriate grill
* We will visit check-out scripts with stops after the holidays

h3. DWSM


h6. +Sphere+

* Sphere dye tested (passed) and is returning from Wah Chang.&nbsp; Arrive tomorrow (Friday) or early next week.&nbsp;
* Much discussion of what we should pressure rate to.&nbsp; Depends on where we send it; 3000m will get to 90% of known vent sites.&nbsp; Port H. can test to 3700m.&nbsp; We will probably not go deeper than 2500m; Chris to talk to other ASTEP PI's.&nbsp; When we see what they want, we'll pass info to Doug, and test for that.

h6. +Elevator+

* &nbsp;Doug finished a 'walk-about' PDR with ship crew about what would work re: elevator design
* CDR for final elevator design; try to do by end of next week.
* Doug has calculated size envelope, weight balance, Center of Bouyancy, Center of Gravity.
* Leveling system should work fine to 8degree slope

*{+}DWSM{+}*
* &nbsp;All tubing is finished; just 4-5 days left for assembly.&nbsp; Progress slowed because of time put into elevator design.

h3. GUI Development

* &nbsp;Nothing

h3. Other Items:

* &nbsp;For January:&nbsp; must revisit puck order for both MOE and for 2 more cores coming along.&nbsp; Also HV puck design.&nbsp; Will talk to Mike Parker about this upon his return.
* Discussed attending JALA for Brent and Scott.&nbsp; Will decide Monday who wants/is willing to go.
* Much discussion about moving our deployment dates.&nbsp; If we can change current schedule, plan is as follows:
*** Dive 1:&nbsp; March 25--no core but elevator, DWSM, sphere
*** Dive 2:&nbsp; April 7-core in sphere, elevator, DWSM-run WCR
*** Dive 3:&nbsp; April 14-core in sphere, elevator, DWSM-minimal chemistry (SHA)
*** Dive 4:&nbsp; May 1-4--plug into MARS (date depends on what we can get that first week)
*** Dive 5:&nbsp; 1-3rd week of May -- pick up from MARS
*** JUNE 8-12--Flyer cruise (these dates may be moved a few days earlier, depending on DMO scheduling changes)
*** AUG 16-26--Flyer to Axial
*** Dive 6: Nov 4--plug into MARS, pickup in early 2010]]></property>
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<property name="body"><![CDATA[In order to manage the data from multiple ESP deployments, a central data repository is required.  This repository needs the following functions:

h5. Requirement
# Provide access over many protocols (HTTP, WebDAV, FTP, SMB)
# Provide authentication and authorization to protect data from ESP deployments
# Provide notification mechanism to alert interested parties when files change and what changes were made.

h5. Design
# File Notification frameworks
## Node.js
### [Watch-tree|https://github.com/tafa/node-watch-tree]
### [log.io|http://logio.org] - For monitoring and send a single file, but might be useful.
### [watch|https://github.com/mikeal/watch]]]></property>
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<property name="body"><![CDATA[h3. Discussion Topics:

+May 27-28 deployment+

Deployment went off without a hitch.&nbsp; Currently Bruce is at M0 and Mack is at Santa Cruz site.


&nbsp;Have had minor issues with over-currenting on PS, and puck sticking in the hand, but feel these problems are minor and will not jeopardize the mission.


+ESP Builds+

Once all parts are in hand, it takes 2 months to construct instrument and hand to science for checkout.&nbsp; This is double what we had thought it takes, but with more assembly experience we have seen the error of earlier (optimistic) estimates.&nbsp;

+2009 Proposal preparations+

Much discussion on what could be accomplished from original 2008 goals. This must be scoped in order to prepare 2009 proposal.&nbsp; Early next week, Jim will get labor estimates on agreed-upon-goals for 2008.


h3. Tech Transfer

* &nbsp;Neo being worked on and will be ready for Science next week.&nbsp; They need to run experiments, as well as we all need a working spare should one of the deployed instruments crash.
* Moe will be the MFB integration machine.&nbsp; Will decide roughly where AIV will be placed, and then Cheri can continue with Moe build.&nbsp; Addie will work with team to decide where to put MFB.

h3. &nbsp;MFB

* Addie has replaced ATV, ARV, all tubing.&nbsp; First slug through the top of the PCR module worked\!&nbsp; Running a second at end of Friday.
* SPE columns:&nbsp; We purchased 3 @ $45; now 3 @ $120.&nbsp; She ordered 8 pkgs of 3 and 3 holders.
* Must run water-quality samples when Chris P. gets back from meeting.&nbsp; Schedule for week of June 16.
* Addie to start building the next MFB ASAP.
* Ball screws have jumped in price because of coating issue.&nbsp; Will talk with Doug about using a different (cheaper) ball screw.
* Spoke of getting device history, esp VICI--how do they handle/treat their valves during/after manufacture?
* Want to be able to save LED data from PCR block; must work with Brent to be able to automatically save the data-object.&nbsp;

h3. Software

* ESP share was backed-up yesterday.&nbsp; Brent making CD of all data.&nbsp; ESP share should be better organized as it is currently full with lots of junk.
* Stopped and re-started Mack to perform a network fix.&nbsp; Should not effect anything since we have 4 down days (next run is Monday evening)
* Next deployment, we will set-up deployment passwords different from lab passwords so no confusion as to which machine you're on.

h3. DWSM

•&nbsp;&nbsp; &nbsp;schedule CDR--set for {color:#ff0000}{*}Tuesday, JUNE 10th.*{color}

h3. GUI development


h3. Other Items

•&nbsp;&nbsp; &nbsp;Planning for 2009 proposal


June 5&nbsp;&nbsp; &nbsp;&nbsp; Have labor #'s for 2008 and have 'nailed' our 2009 projections
June 12&nbsp;&nbsp; &nbsp;Have abstract ready (due July 1).&nbsp; Chris will be gone June 14-July 9? .&nbsp; I'll be gone June 13-June 29.]]></property>
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<property name="body"><![CDATA[Begin forwarded message:
From: Brent Roman <brent@mbari.org>
Date: March 10, 2011 8:30:02 PM PST
To: ESP Technical Deployment Discussion List <esptech@listserver.mbari.org>, "Zhang, Yanwu" <yzhang@mbari.org>
Subject: [esptech] ESP event triggers

I've checked code into CVS that allows mission phases to start on conditional event triggers (per today's demo).

I did add the ability to handle lists of "ored" conditions such that the conditional phase will start when any listed are met, however, I did not add "anded" condition lists because there is no clear definition of what the ESP should do if one of those conditions terminates with an error.  For now, I'd like to propose that we leave this as is.

The example mission is checked into CVS as esp2/mission/triggerTest.rb
It does now synchronize with the CTD polling thread using like this:

{noformat}
:HotWater.denotes proc {
 loop {
   SensorPolling.awaitUpdate
   break if CTD.temperature >= 25
 }
}
{noformat}

Chris P. and I met to discuss how to handle the case where a WCR must be processed on an event that occurs while the MFB grinds in the background.  The current code indeed cannot handle this, as the ESP will not advance to the next phase conditional until the MFB is done.  I intend to remove this restriction in the coming days.

Note that this does not yet include Yanwu's peak detection logic, but is a framework for adding arbitrary conditions to start individual ESP phases.  I'll work with Yanwu next week on converting his Matlab code to ESP event triggers.

-- 
Brent Roman                                   MBARI
Software Engineer               Tel: (831) 775-1808
425 Clinton Street,            Santa Cruz, CA 95062
mailto:brent@mbari.org  http://www.mbari.org/~brent

Here is the script for MOE that the GUI should be able to generate (althought Chris said this is not the final form):
{noformat}
#Mission:  MOE March 2011 M0 Canon
#Nitrate and Temperature can Trigger sampling

module Threshold
  module_function
  def highNO3= highNO3um
    @highNO3 = highNO3um
    log "HighNitrate threshold set to #{highNO3um}uM"
  end
  def highNO3
    @highNO3
  end

  def lowNO3= lowNO3um
    @lowNO3 = lowNO3um
    log "LowNitrate threshold set to #{lowNO3um}uM"
  end
  def lowNO3
    @lowNO3
  end

  def hotWater= tempC
    @hotWater = tempC
    log "HotWater threshold set to #{tempC}C"
  end
  def hotWater
    @hotWater
  end

  def coldWater= tempC
    @coldWater = tempC
    log "ColdWater threshold set to #{tempC}C"
  end
  def coldWater
    @coldWater
  end
  
  def wcrDelay= time
    @wcrDelay= Delay.new time
    log "WCR will wait up to #{wcrDelay} for conditional triggering"
  end  
  def wcrDelay
    @wcrDelay
  end  
end

# initial thresholds
Threshold.highNO3=45
Threshold.lowNO3=5
Threshold.hotWater=25
Threshold.coldWater=2
Threshold.wcrDelay="6:00:00"  #6 hours


:HighNitrate.denotes proc {ISUS.no3 > Threshold.highNO3} #uM/L
:LowNitrate.denotes proc {ISUS.no3 < Threshold.lowNO3}  #uM/L

:HotWater.denotes proc {CTD.temperature > Threshold.hotWater} #C
:ColdWater.denotes proc {CTD.temperature < Threshold.coldWater}  #C

:LowNitrateAndHotWater.denotes proc {LowNitrate[] and HotWater[]}
:HighNitrateAndColdWater.denotes proc {HighNitrate[] and ColdWater[]}
:HighNitrateAndHotWater.denotes proc {HighNitrate[] and HotWater[]}

#standard, repeated mission phase
def pcrWCR(*wcrConditions)
  bacSHAmfb
  awaitEventUntil Thread.time+Threshold.wcrDelay, *wcrConditions
  standAloneWCR ([nil, 1000], $bac) {hotBleach :waste2b}
  Sleep.awaitBackgroundThreads {
    Log.record "Extending phase until #{Sleep.backgroundNames} finish(es)"
  }
end


#$startTime = nil  #don't override start time of initial phase

mission :startTube=>2, :until=>"6AM 5/2/11" do 


  at "1PM 3/31/11" do
    pcrWCR
  end
  

  at "9AM 4/3/11", or: HighNitrate do
    pcrWCR ColdWater
  end

  
end

{noformat}
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<property name="body"><![CDATA[DWSM electrical/software CDR
July 9, 2008

Present:&nbsp; Wayne, Paul, Tom M., Brent, Doug, Scott, Jim B., Chris S.
\\

Comments/questions by audience recorded by Jim B:&nbsp;

•&nbsp;&nbsp; &nbsp;Fuses in power supply lines
•&nbsp;&nbsp; &nbsp;Fan inside ball when power supplies on to help with thermal management.&nbsp; Buy fans that indicate whether they're spinning&nbsp; \--or---&nbsp; Build bigger heat sink and bypass the fan idea.
•&nbsp;&nbsp; &nbsp;Indicator lights for trouble-shooting
•&nbsp;&nbsp; &nbsp;Change connectors to FCR in drawings
•&nbsp;&nbsp; &nbsp;What is input voltage and power supply output voltage?&nbsp; Should you measure output voltage and current?
•&nbsp;&nbsp; &nbsp;Paul's comment on adding nuisance trips
•&nbsp;&nbsp; &nbsp;Hall sensor on brushless high pressure pump motor
•&nbsp;&nbsp; &nbsp;Pressure sensor, can they go to 6000psi?
•&nbsp;&nbsp; &nbsp;Paul, we have the information, but should continue think about failure modes and how will the system protect itself.&nbsp; Like tune motors to torque limit just over getting the job done, in order to tell if job isn't finished.
•&nbsp;&nbsp; &nbsp;Paul mentioned current draw from MARS.&nbsp; Would 20m away cause too much of current drop for Vicor boards to start complaining?&nbsp; Thought is that no, will probably not be a problem.
•&nbsp;&nbsp; &nbsp;Are there cables and connectors to connect to MARS?]]></property>
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<property name="body"><![CDATA[# [Comments from July 9, 2008 Design Review]
# [Doug's collected comments of 9 july CDR]

* [The DWSM scheme |DWSM--4k Deep Water Sampling Module^4k DWSM Operation.ppt] (in particular see slide #3)

New temp insensitive Pressure Transducers arrived 04Sep2009.&nbsp; Testing and installation into D-ESP proceeding for Sep 30 MARS deployment.]]></property>
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<property name="body"><![CDATA[h3. Meeting Held?&nbsp;

Birch at NASA review.&nbsp;

h3. Tech Transfer


h3. Deployment


h3. MFB


h3. Software


h3. Sphere and 4K DWSMS
\\

Doug has leak-tested all combinations of old and new cans/lids, and all have passed He testing.&nbsp; We will keep (and pay for) everything from IMT, despite not getting the requested reports during manufacturing.
\\

h3. GUI Development]]></property>
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<property name="body"><![CDATA[h3. Discussion Topics:

+\-Upcoming May 27-28 deployment+

Decision: &nbsp;Will set out 2 instruments. &nbsp;Mack, and a turned-around Bruce.
Plan: &nbsp;

&nbsp;&nbsp;&nbsp; Tuesday AM: &nbsp;Boat team--Scott, Doug, Chris S.
&nbsp;&nbsp;&nbsp; Tuesday PM: Bruce refurbish team\- Roman, Nilo, Chris P, Doug
&nbsp;&nbsp;&nbsp; Weds AM: Boat team--Scott, Jim, Doug

+\-Personnel Vacations+
&nbsp;&nbsp;&nbsp; Preliminary vacation plans discussed

+\-Board Bullets+

&nbsp;&nbsp;&nbsp; Team asked for pertinent self-promoting items to present to Board.

h3. Tech Transfer

•&nbsp;&nbsp; &nbsp;Lube on ball-screws--grease chosen and all will be lubed from now on
•&nbsp;&nbsp; &nbsp;Radio-modem box leakage--Scott to work on leaking Bruce radio box once mooring is in on Tuesday
•&nbsp;&nbsp; &nbsp;Status of 2nd mooring--not finished, but Scott working on today
•&nbsp;&nbsp; &nbsp;NEO heaters not starting unless power-cycled--issue to keep an eye on.&nbsp; Unclear what is causing it; possible static discharge on dwarf
•&nbsp;&nbsp; &nbsp;Mack hand slippage update--it's been tightened and run in the cold.&nbsp; No slippage.&nbsp; Not an ideal fix, but we don't know what went wrong initially
•&nbsp;&nbsp; &nbsp;Al vs. SS. on valve coupling-\-{color:#3300ff}Aluminum{color} is the chosen material for valve coupling

h3.


h3. MFB

•&nbsp;&nbsp;&nbsp; First successful amplification occurred yesterday with a slug pulled into top of PCR module line.&nbsp; Addie cleaned ATV and input line #13, drew premixed slug into PCR through these; failed.&nbsp; Deconned and repeated yesterday's experiment.&nbsp; Results not [good|^TAM Tests 5_11_08.xls].&nbsp;
•&nbsp;&nbsp;&nbsp; Encoders.&nbsp; Box of extra encoders cannot be found.&nbsp; Cheri put in order for PO # 0810834 to Measurement Specialties for 100 encoders \-\- placed on 4/24/08

h3. Software

•&nbsp;&nbsp; &nbsp;How to avoid vapor lock on first sample after canning the ESP?--Solution decided was to fill line with fluid, then pull vacuum using a syringe to draw bubble back out intake line.&nbsp; Will try tuesday when canning Mack.
•&nbsp;&nbsp; &nbsp;procedures for uploading images from the buoy--Brent implored the use of the 'upload' command rather than pull images directly off the buoy.&nbsp; Otherwise, one must wait for the hourly update of images on ESPSHORE.
•&nbsp;&nbsp; &nbsp;Logging and displaying processed ISUS data

h3. DWSM

•&nbsp;&nbsp; &nbsp;schedule CDR--set for {color:#ff0000}{*}Tuesday, JUNE 10th.*{color}


h3. GUI development

Kevin out of town, but provided this message:&nbsp;

I will be returning from an OOI meeting today so I won't make the meeting.&nbsp; There aren't any GUI updates, but I know I have to change the GUI to output missions scripts in the new format that Brent has specified.&nbsp; I am shooting to have that done next week.
&nbsp;

h3. Other Items

•&nbsp;&nbsp; &nbsp;Planning for 2009 proposal


May 22&nbsp;&nbsp; &nbsp;Discuss the plan for the next 4 weeks RE: 2009 proposal
May 30&nbsp;&nbsp; &nbsp;Note this meeting is MOVED one day, to FRIDAY, due to the Ocean Sciences Meeting.&nbsp; Have 'nailed' our projections for 2008.
June 5&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Have 'nailed' our 2009 projections
June 12&nbsp;&nbsp; &nbsp;Have abstract ready (due July 1).&nbsp; Chris will be gone June 14-July 9? .&nbsp; I'll be gone June 13-June 29.]]></property>
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*{+}First network deployment{+}*

April 3&nbsp;&nbsp;  &nbsp;&nbsp;  Deploy Mack (M0)
April 21&nbsp;&nbsp;&nbsp; Recover Mack&nbsp;
\\

May 1&nbsp;&nbsp;&nbsp; Deploy Mack (M0)
May 12&nbsp;&nbsp;&nbsp; Mack craps out (syringe sticking)
May 15&nbsp;&nbsp;&nbsp; Recover Mack and can swap with Bruce
May 27&nbsp;&nbsp;&nbsp; Recover Bruce
May 28&nbsp;&nbsp;&nbsp; Deploy Mack and Neo (SC and M0)
June 30&nbsp;&nbsp;&nbsp; Recover Mack and Neo


*{+}MB08 Deployment{+}*

October 8;&nbsp; Deploy Mack to Santa Cruz, Neo and Bruce at M0
October 27;&nbsp; recover all]]></property>
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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* Middle of September; Japanese visitor to work on MFB.
* End of Sept for \~3 months;&nbsp; Allison Haywood (New Zealand) to work on a core.
* October deployment:
** Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs).
** there are enough ISUS's for deployment;&nbsp; must test all.

h3. Machine Builds

* Gripper boards are out for fabrication
* Puck sensor boards (10 made) have been modified and {color:#0000ff}{*}Scott{*}{color} is testing on GG in the fridge.&nbsp; Preliminary results look good at ambient (+/\- 1 degree difference from ambient; off 3 degrees at 5d C).
* Mack and Bruce being used (today) by SC group.&nbsp; Should be ready for October deployment with a simple reagent refill.
* Boards:
** 50 Dwarf / 10 Sleepy / 50 R-valve boards are in.&nbsp; Each needs a QC checkout which {color:#0000ff}{*}Dick{*}{color} started on 20Aug2008.
* Much discussion on the number of boards and the NEXT round of builds; could/should we do a board/camera redesign?
* Wiring harnesses are in and QC'd.&nbsp; Many assembled into their 'super-harnesses'.
* Still waiting on small machine parts from El Camino
* Installation of tubing on Moe is next; {color:#ff0000}should take 1 week{color}.&nbsp; Still need to mount AIV on Moe, which was originally scavenged for Neo.&nbsp; {color:#0000ff}{*}Cheri{*}{color} predicts {color:#ff0000}3-4 weeks{color} before Science gets Moe for check-out.
* {color:#0000ff}{*}Cheri{*}{color} will get Mike going on the small hand pieces for Moe's manipulator.

Rough calculations on Mooring Cost:

&nbsp;&nbsp;  Materials/Radios/machined parts/cables/bungee/all parts == $50K + 2 mo's labor

h3. &nbsp;MFB

* Grill is working\! as are PCR scripts
* SPE script is close but syringe continues to have trajectory errors.&nbsp; Much discussion on how to address.&nbsp; Decision to run overnight to 'break-in' and see if sticktion issues are still a problem at slow speeds tomorrow.&nbsp; If that doesn't fix it, we can either gear down motor (but this has problems; fast moves would be slow, mechanical advantage makes it more likely to break something if valve gets stuck), or find a more compatible plunger/barrel combination.
* Stand-alone power boards not yet begun ({color:#0000ff}{*}Scott{*}{color}).
* Go/no-go on PCR for October deployment depends on how PCR does in cold.
* Mechanical changes for NEO to accomodate grill are finished, but scripts need testing.&nbsp; PCR/core group will meet today at 2:00pm to discuss integration.

h3. Software

* Antenna at Novin's (Sunset Dr, Watsonville).&nbsp; {color:#0000ff}{*}Brent{*}{color} and {color:#3300ff}{*}Wayne{*}{color} going out today to scout and sign agreement w/ homowner.
* DWSM code
** starting to test limit-switches; development of this code is on-going
** DWSM code is to a state where we could start testing if we had an instrument.
* {color:#0000ff}{*}Brent{*}{color} mentioned that if the new puck thermal-sensor is super-accurate, then maybe no calibration is needed (the preferred method).&nbsp; Perhaps insulating sensor may add to it's stability/accuracy.
* {color:#0000ff}{*}Brent{*}{color} fixed a core bug.&nbsp; The handling of background threads by using the 'stop' command now works.

h3. DWSM

* &nbsp;{color:#0000ff}{*}Doug{*}{color} spoke with El Camino regarding DWSM parts.&nbsp; Bell housing should finish this week, anodized next week.
* No DMO discussion yet on weight balance/elevator design
* Min-Cons {color:#ff0000}to be ordered{color} by {color:#3300ff}{*}Scott{*}{color};&nbsp; may take awhile because made of titanium (or 'ti-dized')
* Pressure testing;&nbsp; Initially, we do NOT need to got to 4Km, thus we will send/take sphere to Port Hueneme for testing.

NEXT WEEK:

&nbsp;Bring Calendar for deployment planning

Must test new syringes that arrived yesterday&nbsp;]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Bill, Brent, Doug, Scott, Roman

h3. JdF Preparations

* Wand design continues.&nbsp; Doug has ideas for a simple wand/heat exchanger.&nbsp; Will talk to pilots about their wishes.
* Scott discovered that failed encoder in HPP seems to be from vibration breaking wires potted in soft silicon.&nbsp; He's ordered 3 more encoders, and we are have a brace made that will hopefully minimize shaking of the encoder.&nbsp; Doug suggested doing some math on maximum accelerations might explain wires breaking.&nbsp; Could be oil degrading silicon.&nbsp; Still investigating.&nbsp;
* New torque nuts&nbsp; (SuperNuts) have arrived.&nbsp;

h3. &nbsp;Adaptive Sampling and M0 Deployment&nbsp; (MOE)

* MOE deploys in one week.&nbsp; Arrays and PCR looking beautiful, but implementing adaptive sampling causing difficulties.
* Porting Yanwu's code from Matlab to Ruby more involved than initially thought.&nbsp; This adaptive sampling code will not make it on this deployment.
* Revert to simple event detection (triggering on nitrate).&nbsp; First iteration of this code caused major Ruby crashes.&nbsp; This code has been changed and is being tested right now.&nbsp; We must make it through 3 runs to give it stamp of approval.&nbsp; We will know by noon if we continue with this code or revert back to old ESP code without event triggering.&nbsp; Much thanks to Chris P and Brent for hammering on this....
* 'air-battery' containers are at bottom of test tank.&nbsp; Paul C. working on mounting.&nbsp; They should be ready.&nbsp;

h3. WHOI Deployment

* &nbsp;Still haven't pulled connector off 3rd E/M cable;&nbsp; one bolt is stuck.&nbsp; If it breaks, cone is ruined.&nbsp; Roman working this.
* Shipping option has been selected.&nbsp; Temp controlled truck arrives for loading April 1.&nbsp; Will arrive at WHOI April 7 or 8 into Roman's waiting hands (he fly's out the 6th).&nbsp; This shipping option costing \~$7K.&nbsp; We will need a place to store our totes at WHOI (no van is being left behind).
* Doug ordered cushioning material for ESP can.&nbsp; Will get Greg Voogd to help build a 'floor' that will sit in palletainer.
* Roman has sent out paperwork for He leak detector rental ($700/week).&nbsp; They will ship it to WHOI; we'll have for 3 weeks.&nbsp; WHOI has He and N2 and regulators.
* Deployment plan:
** Leave WHOI as early as possible Tuesday, April 19.&nbsp; Arrive at NH Science center dock that evening.&nbsp; Sleep on boat.&nbsp; Early AM, April 20, divers arrive, get on boat.&nbsp; Motor to site and deploy.&nbsp; Do some water casts around ESP while we make sure it's working.&nbsp; Return divers to dock and continue water sampling transect.&nbsp; Begin return to WHOI early

h3. G3 Development

* Spoke with Jim Bellingham about a 2foot section on front of LRAUV.&nbsp; He suggests we do a quick remodel with his fluid dynamics guy.&nbsp; Email introduction has been made.&nbsp; He has also thought of the possibility of scaling the AUV to be bigger....sigh.

h3. Drifter

* Design review today at 1pm.&nbsp; Brent leads discussion of communications and networkability.&nbsp;
* Our Satellite Phone account has been set up yet we have not rec'd any bills for the monthly fee.&nbsp; Brent to send contact info to Jim to deal with this.]]></property>
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<property name="body"><![CDATA[Present: Jim, Chris P, Roman\\
* Quick discussion of MOE preparations.&nbsp; Deployment on Thursday this week.&nbsp; Plan to meet Scholin at noon to discuss the mission plan w/adaptive sampling for this M0 deployment.
* Discussion of Chris's vacation and Romans departure for WHOI April 6.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Bill, Elif, Brent, Chris P, Doug, Scott, Roman, Chris S.

h3. JdF Preparations

* Parts for wand and temperature sensor are either ordered or have arrived.&nbsp; Build and design of wand continues.&nbsp; Temp probe tips have arrived and have been pressure-tested.
* encoder in HPP seems to have failed (again).&nbsp; Either because oil gets on it or some unknown electrical issue.&nbsp; Scott working on this problem.
* Doug awaiting new nuts that relieve us of having to use special torque wrench to get to recommended torque when closing DWSM for high-pressure testing.&nbsp; These should arrive tomorrow or Monday.&nbsp; Then high-pressure testing should commence (if HPP fixed).
* Bill has a straw man crew list for JdF [here|^Juan de Fuca Science Crew List.doc]

h3. &nbsp;Adaptive Sampling and M0 Deployment&nbsp; (MOE)

* Ran 1st integrated run yesterday; water very stinky and PCR was inhibited, but mechanically ran fine.&nbsp; Array was good.&nbsp; Starting 2nd sample tonight.&nbsp; We want 3 good runs in a row to say it passes qualification.
* Will set up MOE with ISUS and CTD to begin lab testing of adaptive sampling on Monday.&nbsp; John R. taking care of the ISUS cleaning/preparation.
* Brent to receive Yanwu's code on Friday and might work on over weekend to get it into 'ESP-speak'
* Deployment has been moved UP to March 31.&nbsp; Although this makes for slightly longer deployment we thing no problem with power and # of samples.
* We are using the 'air-battery' containers for this deployment (not orange boxes).&nbsp; Almost finished, but must check who is making brackets for mounting these.

h3. WHOI Deployment

* &nbsp;Currently we have 3 E/M cables.&nbsp; in meters: 15a, 15b and 20.&nbsp; The 20m did not ohm, and we found water and corrosion in one connector.&nbsp; That has been cleaned and 'resealed' with lots of silicone grease.&nbsp; 15b passed the ohm test, but showed some funky readings (i.e., not perfect).&nbsp; 15a works, and debate was whether to pull it apart.&nbsp; Decision was yes, pull, inspect, and grease.&nbsp; We will use this shortest cable (15a) for WHOI since there's lots of activity in the area of the mooring (lobster pots).
* WHOI to provide their own batteries, but we should test their polarities.&nbsp; Also make sure they have an interface cable if we're doing a hot-swap.
* Brent heading to WHOI on March 27.&nbsp; 2 days setting up shore-station, and 3 days assisting EOM/McLane in getting ESP to talk up their gumby.
* Roman working with Doug to see if we can rent a He leak detector while at WHOI.
* Various shipping options are being explored with the help of Teresa Cardoza.
* Kevin Gomes will meet with Chris P, Roman, and Elif to discuss the latest incarnation of the mission planning software.

h3. G3 Development

* We will have a G3 meeting next Tuesday at the normal ESP Science meeting to discuss some discussions that Doug/Scott have had.]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument and the various places it will live.  The ESP directory structures contains the following:

# /var/log on the linux host is the root directory for the FTP site (i.e. = ftp://espName).
# /var/log/messages contains linux kernel messages
# /var/log/vsftpd.log records all FTP site traffic
# /var/log/$USER is top level output directory for each user's ESP data (can be overridden with $ESPlog variable, but this is rare)
# Content in /var/log depends on configuration, but default is:
## _hires_: high resolution camera images (each approx 3.5 MB)
## _lores_: low resolution camera images
## _midres_: medium resolution camera images (typically autoexposures)
## Top level directory contains default resolution camera images (typically fixed exposures)
# Only files in top level directory are uploaded to shore
# File types are:
## *.tif = TIFF camera images
## *.pcr = Comma Separated Value PCR Data
## *.out = Console output capture
### Text normally output to the esp interactive console
### Redirected here when running non-interactive mission script
### Can be viewed with showlog command
### File is named after operating mode (real, sim, simreal, quick)
## *.log = detailed, binary esp engineering logs.  The file is named after operating mode (real, sim, simreal, quick).  Can be viewed with dumplog.
## *.tube = list of carousel tubes processed
### One tube per line, last line is the currently active source tube
## ISUS*.err = ISUS error messages (direct from the ISUS)
## ISUS*.dat = text records of the ISUS data (complex and incorporates CTD data)
## CTD*.hex = CTD data in hexidecimal formatted text records
### Seabird specific format

NOTE: Brent wrote up some instructions on parsing the log file [here|ESPAPP:Parsing the Raw ESP Log File Format]

The initial thought about how a complete data management system might look is:
{gliffy:name=ESP Data Overview|space=ESPAPP|page=Design|pageid=6258757|align=center|size=L}
{panel:title=Things to note}
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station (this includes the ruby scripts used to run the ESP).
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.
{panel}


So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

So, in order to manage this synchronization and storage of data, it was decided that the GUI would be reponsible for that synchronization.  Initially it would be a manual process as it will be time consuming and the user should be responsible for firing it off.  Then, once it is solidified a bit, it would be nice to push it back to a background thread that happens automatically.  The GUI for this synchronization, might look something like this:

{mockup:Data_Import|1}


Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

||Mockup||Notes||
|{mockup:Top Level|12}|A mockup of what the user might see upon first starting the application.|
|{mockup:InstrumentSelect|3}|Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?
Here is the mockup showing what might happen if the user selected one of the instruments.|
|{mockup:DeploymentSelect|3}|After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times|
|{mockup:MouseOverEvent|2}\\{mockup:EventDetails|2}|In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open.|




There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[h3. Normal Science meeting was usurped by discussion of progress on G3 development.

Doug led meeting with progress to date on design approach.
* Took a Systems Engineering approach, which focuses on the _functions_ we are looking for.

h4. &nbsp;What do we currently know:

# Volume of G2 components
# G3 target and margins (considering a 2' extension to the LRAUV)

{gliffy:name=volume margins|space=ESPAPP|page=ESP -- SURF Center Main Page|pageid=2162822|align=left|size=M}
Right now, dry housing will hold 20 liters&nbsp; (current surface can is \~200 liters)

3. G3 system design by function
\--this is Doug's "design dependencies" slide
4.&nbsp; Has 'cost' spreadsheet; helps predict leading costs--currently is Volume.&nbsp; This model was run on G2 and came up with 171L, close to can's 210L)
5.&nbsp; First run on G3 concept has run through the predictor.

h4. Concepts developed

1.&nbsp; Fictional G3;&nbsp; this is the solidworks model everyone has
2.&nbsp; Pizza slice idea

h4. Refinement of Functional Requirements

Some things we still need to know:1.&nbsp; What contextual sensors will be on the AUV?&nbsp; CTD?&nbsp; ISUS?

2.&nbsp; LRAUV needs some 'payload' space in order to fly. (ADCP, compass).&nbsp; How does that cut into 'our' space?

h4. &nbsp;Designs we have chosen to bring forward

1.&nbsp; Linux/Ruby
2.&nbsp; new CPU (Brent has chosen)
3.&nbsp; Reuse Dwarf cards bu change CPLD to FPGA
4.&nbsp; Will use power from vehicle, but they have not provided a power budget.
5.&nbsp; Mechanical:&nbsp; Must validate the extension of the AUV&nbsp; (NOTE: contacted Jim Bellingham who suggested working with their hydrodynamic modeler.&nbsp; Awaiting contact \[3-22\])
5.  We are going with one pressure housing and a liquid barrier wall between ESP and drive compartment.

h4. Cube/Filter testing

1.&nbsp; We need a solid baseline to compare filter efficiencies.&nbsp; Will begin with millipore water.&nbsp; When we move to particulates, it will require much empirical work to define trade space and decide.

2.&nbsp; Should also think of fractionation, as scientists will want to analyze many size fractions of filtrate. ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Bill, Doug, Roman, Scott, Chris S., Chris P., Yanwu, Elif

h3. Adaptive Sampling

# &nbsp;Question is, how do we spend our 40 samples during this spring's M0 deployment?
## We will consider two scenarios:
### high nitrate, high salinity (an upwelling event)
### rising nitrate, dropping salinity

The thought is to trigger on high and low nitrate peaks/troughs.&nbsp; We are not moving the 'instrument' so can't use yo-yo methodology.&nbsp; But can use tidal cycle.&nbsp;1.&nbsp; Must track long-term background nitrate levels.&nbsp; Then, peaks are defined as 1.5x higher than background.

2.&nbsp; Also can compare to average peak height over last 7 days (e.g.).
However we trigger, there will be a 1-day lockout time.&nbsp; Then a control sample every 3-4 peaks where nitrate is lower than monthly average by 1/2.
\[\]

3.&nbsp; The second part of this deployment is related to CANON, and we'll do an archive and a full phase, and we KNOW the event is coming.&nbsp; Thus, ESP waits until threshold is reached and hten it fires when water mass is over it.&nbsp; This is fundamentally different than the scenario above in 1&2.&nbsp; Chris Preston summarized these two approaches in the below graphic.
\\  !SpringM0deployment.png|thumbnail!

In the last 2 weeks of the deployment, there's enough time to do 15 "events".
\\

h3. &nbsp;WHOI Deployment Issues

&nbsp;1.&nbsp; Current location is 8.2nm offshore.&nbsp; WHOI wants the EOM buoy near the NH buoy.&nbsp; This is untenable with our surface expression design. Could we raise our buoy?&nbsp; Talked about using EOM mooring as a repeater.&nbsp; Lots of issues.

Ideal case is we are in a place where we are our own entity. &nbsp;

May raise shore station antenna; will talk to WHOI>

Will check to see if WHOI can provide 800+lb anchor so we don't need to ship. 2.&nbsp; Must talk to Theresa to begin the shipping issue.&nbsp; We will be  sending ESP-Bruce, a surface mooring, and many spares (bugees, etc.)2.&nbsp; Began discussion of shipping container needed.&nbsp; Maybe a 10' one, half our current van size?&nbsp; It will need to be temperature controlled.&nbsp;&nbsp;

h3. Jdf

1.&nbsp; Electronics box is the difficult.&nbsp; We've found a pressure housing but unclear about connectors.

2.&nbsp; The minimal setup would be a temperature self-logger; still waiting for one to arrive from Pete.

3.&nbsp; Brent to talk to data-logger builder to understand how to communicate with it.

h3. Local Machines

1.&nbsp; Bruce has had high temp calibration.&nbsp; Then needs QC test.&nbsp; Then full-phase testing @ appropriate temps.

2.&nbsp; Roman will start assembly of MOE tomorrow.&nbsp; Chris P working on Moe's MFB. ]]></property>
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<property name="body"><![CDATA[h4. (as of April, 2015)


h1. Surface Mooring Cables

*35.5m (w/ floats)&nbsp; (DESTROYED)*

* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).
* del mar 6 month (summer 2016)

*25.5m*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

*21.5m (BAD)*
Now with bad connector...&nbsp;
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos in the attachments of this page.
* late-2014; was this EM cable repaired?

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)
* Moran deployment (Sept/Oct 2016)

*15.2m (BAD; bad BSR?)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]

\\

All shockles modified Dec 2015 to be like 001 (stretchier cords)

h4. ESP-001 (modified with 'stretchier' cord)

* 44 days during Catalina (April 2014) deployment
* Moran MB deployment (Sep/Oct 2014)
* ECOHAB?
* Del Mar (start May 17, 2016)

h4. ESP-002

* Moran (sep/oct 2016)

h4. ESP-003


h4. ESP-004


h4. ESP-005


h1. Anchor lines

\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4. *57M*

* 2014 Moran deployment in MB
* moran (sep/oct 2016)

h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\
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<property name="body"><![CDATA[Present:&nbsp; Jim, Bill, Elif, Brent, Chris P, Doug, Scott, John, Roman

Absent: Chris S.
\\

h3.


h3. JdF Preparations

\\

1.&nbsp; Doug sent out the following schematic for the wand design:
\\  !JdeF Wand.png|thumbnail!
* Pete had some questions about wand height and how adjustable it might be in a rocky, uneven environment.&nbsp; We will get the pilots involved in these discussions.
* ISMS--Charles still working on it.&nbsp; They will send to us by the {color:#ff0000}end of April{color}, if not sooner.
* Berthing:&nbsp; Who is going on the cruise is still TBD.&nbsp; Harvard would like 3 berths (2 male, 1 female)--if there is room Dan Rogers might like to go.&nbsp; There was also suggestion to bring Karen Loyd for the ride (if room).&nbsp; Bill U. is working on this list and we will discuss at next week's science meeting.
* do we want Pete's mass spec temperature logger?&nbsp; Yes.&nbsp; He will ship.
\\

h3. &nbsp;Adaptive Sampling

&nbsp;Brent has created a simulation and provided a great demo of the code that triggers on certain contextual thresholds.&nbsp; He rec'd some input from Science on some tweaks.&nbsp; Yanwu returns next week, and he and Brent will work together to put Yanwu's code into Ruby.

h3. M0 Spring Deployment

* Chris and Roman making excellent progress
** MOE will have reagents by end of today
** MFB gets mated on Monday
** QC tests next week
** Week of March 21 we'll test adaptive sampling
** Can on April 1
** Deploy April 7

* There was some discussion of the Zephyr also deploying another instrument at M0, using our cruise.&nbsp; Will check on this.

h3. &nbsp;WHOI Deployment

* &nbsp;All systems moving forward.&nbsp; Turner Calvis (?) is the guy to contact at UCONN regarding divers.&nbsp; Roman is on this.
* We have selected site #3 as our deployment site. 4.3nm offshore and 113 ft depth Lat - 43.0347&nbsp;&nbsp; N; Long - 70. 6172 W
* Notice to Mariner info has been given to Mike Kelly.&nbsp; He is waiting for contact person from WHOI in order to submit.

 !ESP locations_2011v14_3_9v2.png|thumbnail!

h3. D-ESP

* DWSM has been reassembled but not torqued closed for high-pressure testing.&nbsp; We've ordered our own set of tools for that.&nbsp; Also found that the empty switch in the sample can does not work.&nbsp; This will need replacing, but high-pressure testing can continue before tearing everything open again.&nbsp; Must be careful not to squeeze the bag empty.

h3. &nbsp;Drifter

* Will have a meeting of Brent, Scott, and Gene on Monday, 2pm.
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<property name="body"><![CDATA[Present:&nbsp; John, Julio, Elif, Bill, Chris S., Jim, Chris P

Absent:&nbsp; Roman
\\

h3. Core ESP preparation

* &nbsp;ESP-Bruce is about to start the 2nd of it's 3 pre-deployment runs.&nbsp; Hopefully finished with all on Friday, and we will be ready for canning.
* &nbsp;ESP-MOE has had MFB qualified and all reagents are loaded.
** One worry is no runs have been performed since the rebuild.&nbsp; Tonight will run core-negative, tomorrow pressure tests, next week will fold in software changes for adaptive sampling.&nbsp; Then test with spiked nitrate to test the algorithms.

Array Printer causing problems--this time alignment issues.&nbsp; Roman will investigate when he returns.

h3. BioSpace and SHA

* &nbsp;Discussed how we can put our results in the larger group context for the meeting planned March 28-30.
* Julio has run 32 gulper arrays for zooplankton, and tying to push to get 30 HAB's finished.
* John/Julio/Roman/Jim/Chris will meet to discuss how to put ESP data in line with hydrographic data and figure out how to present.&nbsp; This meeting will be Weds or Thursday this week.

h3. Other issues

* &nbsp;NSF coming March 21 to film ESP stuff.&nbsp; Kim Fulton-Bennett organizing this.
* Much discussion about what our next 3-18 months look like:
** Elif
*** develop p/p for HAB species
*** compare SHA results with qPCR results for HAB species
*** once p/p developed, apply these to transects from Chavez cruise
*** apply and help with prep for JdF, and SC Wharf
** Chris
*** Prepping MOE for spring M0 deployment
*** Optimizing Harvard's probes for JdF this summer
*** Conversion of NEO to a grill-style MFB and the associated code changes and testing that will require.
*** Get NEO working to run HAB/DA/qPCR from same sample for testing on SC Wharf in fall, 2011
*** perhaps rubisco gene development for D-ESP on MARS in Fall
** Bill
*** will return to process our multitude of archival samples
*** continue to learn MFB processes with goal to set up D-ESP MFB work for MARS in fall, 2011
*** continue as logistics coordinator for JdF this summer
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<property name="body"><![CDATA[h3. Deployment Update

* Jim Crisman has moved up his available dates.&nbsp; Means we must MOB Tuesday (Oct 7) and deploy Weds (Oct 8).
** M0--Bruce with new CTD
** M0--Neo with old CTD and ISUS
** SC--Mack with old CTD and ISUS
* Will run room-temp big pahse (PCR w/ LAF Bac concurrently) this afternoon.&nbsp; This is the PCR + WCR phase; 20\+ hrs.
* Brent still working on&nbsp; PCR/BAC integration
* For the entire deployment, NEO is doing only PCR/WCR and BAC/WCR
* Discussed the schedule (27th would be + cold, 28th would be - cold, 29th would be + cold)
* Running in cold we will use it in box, w/ ISUS and old CTD.&nbsp;

h3. Machine Builds

* Doug assembled harmonic drive on lathe for 'perfect' alignment.&nbsp; Power comparison to be performed this afternoon.&nbsp; We may have to redesign this with 2-shafted harmonic drive which will necessitate a different motor mount for the elbow joint.
* Puck temperature sensor on Moe-need more of them.&nbsp; Jim Montgomery can do this.&nbsp; Mounts for these are old--we need the newer sliding mounts.
* Ball screws-NOOK only made rev. D, which, according to our drawings WAS too small for us, but these seem as tight as the rev. E.&nbsp; Unclear what drawings they have (they say they've always built to rev. D drawings), so we must be very explicit in future orders-put rev on PO and call them for verbal confirmation.
* Dwarf Boards:
** have tested 15 of 35
** curious:&nbsp; after hand is closed, we still have voltage to the gripper drive.&nbsp; Must look into this after deployment.
** Will be finished by end of next week.

h3. MFB

* Syringe has been losing it's encoder position and over-filling until it hits the hard stop and overcurrents.&nbsp; First time, it pulled black plunger end off.&nbsp; Syringe has now been replaced and recalibrated.
* Still don't know reason; maybe losing encoder counts (9-30: yes--bug in Xylinx upgrade software seems to cause it; have reverted to older version and problem is gone)&nbsp;

h3. Software

* New CTD's have different firmware.&nbsp; Nontrivial.
* CS syringe on NEO has been changed
* Bruce--got stuck last night.&nbsp; Anytime tried to move a syringe or valve it hangs.&nbsp; It waits for a thread that's already dead.
* Mack--PS and clamp got corrupted (overcurrent errors).&nbsp; Sent out a 'recover' and it fixed it.
* Can't seem to FTP into shore station from his house
* Radio tests worked well, but while one file is uploading, link is monopolized (we can't talk to the other machines)
* Will give radio's to Jose
* Home syringe has been renamed.
* Firmware code still not frozen until Brent fixes: 1.&nbsp; Recover from hang due to dead thread, 2. Link protocols fixed, 3. CTD changes made

h3. DWSM

* Sphere on lathe at Tapemation
* Bulk-heads (swiss cheese plates) awaiting their turn in our shop
* Doug has some parts to be made; will give to Larry or Jose

h3. GUI Development

* &nbsp;Kevin working with Chris Preston on the new 'killer' mission planning app
* data analysis software being worked up right now.

h3. Other Items:


h5. Container:

* We will PURCHASE a container, but defer to future.&nbsp; Container information is here

h5. Build Schedule:

* &nbsp;Doug unsure if we will be ready for deep ESP testing in first week of January.&nbsp; Issue is that they are setting Lobos days for 2009, and we are slated for 5 days; they want us to take&nbsp; 4 days in Q1 and Q2, and they'll through in the 5th somewhere.&nbsp; We need a schedule from Doug on how the D-ESP testing will proceed with the ship days.&nbsp; Original plan was to start with passing fluid through the sphere, working toward a WF deployment before the big Axial trip.&nbsp; Doug should get a WAG schedule by end of day.

h5.

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<property name="body"><![CDATA[h3. Deployment Update

* October deployment:
h6. {color:#ff0099}Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs){color}

* {color:#000000}Mission is defined for NEO.&nbsp; Still to do for Mack and Bruce but should be straightforward{color}
* {color:#000000}Small Array format being difficult.&nbsp; Will make call by end of day today on whether we can make it work;&nbsp; we're very close, but may punt on it.{color}
* {color:#000000}If it works, need Brent to work on software integration.&nbsp; He may work on it over weekend.{color}

h3. Machine Builds

* Moe--elbow still not working.&nbsp; Scott conferring with engineers within company.&nbsp; Mike working on putting counter-bore into holder piece which may help alignment.
* Moe should be ready by Oct 13 visitors.
* Bumper for NEO ready
* Board checkout--Dick got host board.&nbsp; We need some dwarfs so Cheri/Addie may quickly check 2 out.&nbsp; Cheri will show Wayne how checkout works, tomorrow.

h3. MFB

* Much discussion of stand-pipe issue.&nbsp; Decision was to not change what works, since it hasn't loosened since people have stopped messin' with it.
* Brent fixed a problem with the serial cable from the PCR module to the dwarf; power cycling is no longer a problem
* Have had 2 time-out errors with the AS; it loses its position but dwarf is not reset.&nbsp; Brent will try upgrading firmware from v.2.50a(64Hz) to v.2.59a(64Hz).&nbsp; If this doesn't work, we'll try a new dwarf.
* Bruce 'brain-freeze' may have been a network problem.&nbsp; Brent changed from CAT 3 to CAT 5 cable in the B-lab.&nbsp; Still watching for hangups.
* Addie contacting PCR-tubing company for a remake; in meantime we will NOT be asking LLNL for more tubing, as it appears the current tubing works.

h3. Software

* Would like to freeze Mack/Bruce code by tomorrow (Friday).&nbsp; Start radio tests next week.&nbsp; Must exercise all assays to check out.
* Many chunks to stitch together for SAF to work on NEO.&nbsp; Much discussion on how long that may take and how much cutting into our cold testing is acceptable.&nbsp; Chris working with roman and brent on this.
* should re-name 'home syringe' on MFB (Addie).&nbsp; Discussion finalized a solution.
* Brent discovered they don't make the old CTD's anymore and there is question as to whether our drivers will work with the new CTD model.&nbsp; Decision is to use old CTD's on Mack and Bruce.&nbsp; We then can 1) borrow another older model, 2) use the deep CTD (with wacky pressure gauge), or 3) get a new one and hope drivers work.
* Brent working on firmware today and will hand-off HEX files to Wayne

h3. DWSM

* Drawings for both plates finished and gone over with Ray
* Estimate is that Ray will be working on these until October 23
* Oatmeal can is now called the Thermos, and is finished
* Bell housings are here and check-out.
* Burn-rates on ASTEP and NSF are acceptable; if we need more shop labor time, Chris S. can charge less to grant.
* there is one piece of pressure testing for DWSM that is $6K.&nbsp; Approval given to purchase.

h3. GUI Development

* Kevin out sick today, but stated the following in an email:Jim, the ESP GUI should be ready for the mission planning exercise tomorrow and I will work to finish it up today and roll it out to production tomorrow AM.&nbsp; I can then work with Chris P (or whomever) to do the mission plan.&nbsp; I have started on the data access part and am hoping to have something working over the next couple of weeks before the deployment ...

h3. Other Items:

* _Oceanography_ paper came in 6 pages over length limit, so we are not including photo of MFB mounted to core.&nbsp; Photo-shoot next week is canceled.&nbsp; Chris is editing down...
* Research on renting a storage van has begun.
* The heavily load in support engineering was explained to the ESP team.&nbsp; Mark would love 30-days advance warning as many disparate projects have come due in Q4 and Q1, 2009.]]></property>
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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* October deployment:
** h6. {color:#ff0099}Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs){color}

h3. Machine Builds

* AIV mounted into Moe
* Elbow still giving problems with sticktion.&nbsp; Cheri and Scott have spent 3 days working on it, yet it still needs 2x the current of the elbow on NEO.&nbsp; Much discussion of what may be the problem.
* Will do a quick can-test this afternoon of NEO with the MFB attached.&nbsp; Will build delrin stand-off to help guide core into can.&nbsp; Addie to talk to Mike P. about this.
* {color:#000000}Dick{color} has checked all Sleepy boards;&nbsp; now needs a host board.&nbsp; Brent will work with Wayne MONDAY to generate a host.&nbsp; Will get to Dick by TUESDAY.&nbsp; Meanwhile, Dick is moving on to testing dwarves.

h3. MFB

* Addie to work on a +mechanical+ solution to the loosening of the mixing stand-pipe.&nbsp; Will not use silicone.
* Will size-test in can this afternoon
* Must connect PCR-module to dwarf via serial cable.&nbsp; Brent has cables; Addie will get and handle config file changes to make it work.
* Delrin stand-offs; talk to Mike P about design.

h3. Software

* Current versions:
** {color:#ff6600}&nbsp;FIRMWARE{color}
*** 2 Dwarf 'flavors':
**** v 2.59--Standard on all dwarves (some dwarves on NEO have 2.58).&nbsp; ALL CORES WILL BE UPGRADED TO 2.59 before October deployment.&nbsp; All dwarves Dick is testing are being loaded with 2.59
**** v.2.5a(64Hz)--special version for MFB dwarf ('a' version has debugging feature removed)
** {color:#ff6600}RUBY{color}
*** Mainline Ruby is on Bruce and Mack
*** A branch is called MFB/NEO--\- this version modifies 3-4 files unique to NEO
** {color:#ff6600}LINUX{color}
*** Mack & Bruce using v1.6---which has slight communications change from NEO.&nbsp; NEO will be upgraded to v1.6 so all running same LINUX.

* Also, a 2nd puck evac added to BAC arrays.&nbsp; Worry is that code is not tested.&nbsp; Chris S. will start testing on Bruce & Mack this weekend.
* Stitching of 'superphase' code will commence early next week (Monday).
* Wayne will work on getting up to speed on our board structure, and set-up a procedure to make board-burning more accessible to the layman.
* Wayne will work on getting firmware into HEX format so easily accesible to all.
* Tracking ESP Boards
** Wayne asked what people wanted to track.&nbsp; He has good idea of variables and will work with technicians to build a MS-Access database to track board builds, and firmware changes on those boards, etc.
* All parts in for antenna installation tomorrow.&nbsp; Scott building a kit for Brent to reterminate cable.&nbsp; Meeting at Abol's house @ 1:00pm.&nbsp; Mounting bracket should be finished by 1 today.
* Tested radio system on Mack.&nbsp; Something wrong because data from buouys can't find the WWW on-ramp..&nbsp; Brent will try and fix this PM; otherwise will work on after antenna installation.

h3. DWSM

* &nbsp;Bell housings should be delivered to MBARI Tuesday.
* Oatmeal can is \~75% finished
* Sphere needed updated drawings--more detail for machining.&nbsp; Doug stopped them from welding holds on the hemisphere and provided ports to hold piece.
* Big purchases coming:&nbsp; Swagloc/Min-K/Electrical fittings
* Must talk about $$ and burn rates in ASTEP/NSF/MBARI
* Doug needs 7 valve-motor mounting parts.&nbsp; Will take from MFB stock, but must re-order/remake.
* Doug has been working on Solidworks assembly drawing for the _Oceanography_ paper.

h3. GUI Development

* Mission GUI.&nbsp; End of next week all compononets should be in mission script GUI.

* Mission state software very expensive, and licensing is labyrinthine.

h3. Other Items:

* Photoshoot of MFB mounted on core will be Tuesday, Sept 23.&nbsp; May mount grill to GG, to minimize impact on team.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Gene, Julie R., Chris P, Chris S., Elif, Jim
# Much discussion (preliminary) about logistics for shipping ESP to Hawaii in September Drifter Experiment.&nbsp;
## Decisions:
### We will ship in a chilled cargo van with all reagents loaded here in CA; the van will be loaded directly on the Kilo Moana.
### Must get shipping prices for such a van, and
### What are power/plug requirements of K/M?
## Also may want to get air freight prices, just to compare.
## Mission to be downloaded before we ship instrument.
## Julie to begin thinking about the number of samples we will run, given mission length.
## Gene thinks 3 people would be ideal to monitor drifter, especially if ESP team is not pulled to do other work;&nbsp; Julie doesn't think they will be, as Zehr and Church teams will be complete to do their own thing(s).&nbsp; Current plan is Gene, Roman, Julie.
# discussed how to adjust MOE's adaptive sampling strategy.&nbsp; Chris P. has a plan for this 'trial' week.&nbsp; She'll push down new mission tonight.
# ESP-Bruce has left Chicago and should arrive @ WHOI Thursday.&nbsp; Roman flies out tonight.]]></property>
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<property name="body"><![CDATA[Add seawater sensors at bottom of each oil chamber
Sample tube in bag to ¾ depth
Upper/lower purge may need to wait until, or be moved to after sampling.
May need to add an RO water rinse fluid. (non-toxicant) Verify that air compliance is at right volume.
Also look at cast 17-4 for bell housings.
brent:&nbsp; One could use a serial port or ethernet for communications to the ESP
brent:&nbsp; Core must be work from 2C to 35C
gene:&nbsp; Test urathane bags for oil compatibility
gene:&nbsp; Pack toxicant bag in PVC or similar hard container
gene:&nbsp; Don't servo on pressure, just monitor it during decompression
brent:&nbsp; measure amplitude of sample pump's pressure impulses
brent:&nbsp; Modify ESP scripts to purge into DWSM before starting sample processing
gene:&nbsp; Add an external bag for DI Water to mix with toxicant
brent:&nbsp; Add filter on raw water inhaled into bags when rinsing them
brent:&nbsp; Measure compliance when filling bells with oil
jon, gene, et al.:&nbsp; Invert bells when filling with oil
gene:&nbsp; Dish out top plate to control air bubble size
gene:&nbsp; consider stainless for casting bell housings
jon:&nbsp;&nbsp; 3 threads on HP oil pump motor housing is bare minimum
gene:&nbsp; O-ring on HP oil pump motor housing may be damaged on assembly
mike:&nbsp; put O-ring on inside wall to prevent this &nbsp;
&nbsp; Need fuses on power
* &nbsp;&nbsp;&nbsp; Yes I do need to add then and I will

Need to add fan for 600W
* &nbsp;&nbsp;&nbsp; See last comment in this paragraph

Consider indicator lights
* &nbsp;&nbsp;&nbsp;&nbsp; I will consider

Monitor input and output voltages
* &nbsp;&nbsp; I need to investigate how to do this within the current hardware

May need to mointor fan operation
* &nbsp;&nbsp; consider this

Also, size internal heat fins to hold heat of 1 decomp. &nbsp;
&nbsp; Pressure switches, use NC instead of NO since most tend to fail open as opposed to fail closed.
* &nbsp;&nbsp; good suggestion, CPLD allows for this change in logic state

Not much margin over 4000m on PT's, check the % over reading capacity.
* &nbsp; While we may not be able to read to the actual full depth ocean pressure this is not a big concern as we are mainly concerned that

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; we have decompressed to a save level.&nbsp;Since we use a compensation chamber we do not pump to pressure.
Plan to test fault conditions &nbsp;]]></property>
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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* October deployment:
** Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs).

h3. Machine Builds

* Problems with Mack and Bruce have been resolved since SC visitors.&nbsp; Thanks to work by {color:#3300ff}{*}Scott{*}{color} and {color:#3300ff}{*}Roman{*}{color}.&nbsp; Still noticed forearm slide on Mack needed to hammer each time.&nbsp; This issue should be resolved in next build when we use different slides.
* Still need to mock-up and test new communication protocols to be used during October deployment.&nbsp; {color:#3300ff}{*}Jim{*}{color} will check with Science to see when machines are free for this.
* {color:#3300ff}{*}Scott{*}{color} still working on testing puck sensor boards when he has time.&nbsp; These will not be implemented until after Oct.
* MOE update:&nbsp; easiest to plumb from inside out, and {color:#3300ff}{*}Cheri{*}{color} still waiting on the custom AIV stator cap.&nbsp; Thus, plumbing put aside and she's been building manipulator arm;&nbsp; mechanical work finished, finish wiring today, start testing; hand should be finished early next week.
* 3rd Mooring:&nbsp; all parts are fabbed.&nbsp; {color:#3300ff}{*}jim S{*}{color}. will start building next week or as soon as his immediate FOCE duties are finished.
* {color:#3300ff}{*}Dick{*}{color} checking Sleepy boards, has not started on dwarves yet.&nbsp; As a way to get up to speed, {color:#3300ff}{*}Wayne{*}{color} will insert himself into the QC process of sleepy and dwarf boards.&nbsp; Scott noted that Dick may have jury duty Sep 15/16.

h3. &nbsp;MFB

* {color:#3300ff}{*}Mike P.*{color} has started looking at mounting tombstone (TS) to NEO.&nbsp; Should be mounted by end of next week.
* Grinding noise of ATV was deemed inconsequential.&nbsp; Much discussion about removing detents from valves.
* Sealing around mixing column was discussed.&nbsp; This should be something Chris/Addie/Jim/Scott brainstorm about.
* {color:#3300ff}{*}Addie{*}{color} and {color:#3300ff}{*}Chris P{*}{color}. working on test-plan for MFB/NEO integration.
h3. Software

* Due to Wayne's knee surgery, antenna mounting moved from Sep 6 to either Sept 12 or 13.
** Plan is to make 1 visit.&nbsp; Brent assembling parts necessary and will bring extra router in case we cannot access the one on-site.
* We will clone the 'server' in Brent's office (Bufflehead) to a machine lifted from A244 Lab.&nbsp; Wayne can then use this in his testing of boards.

h3. DWSM

* &nbsp;Bell housings have just been turned, ports cut, and may have to be sent out of state for anodizing.&nbsp; {color:#3300ff}{*}Doug{*}{color} will lean on El Camino...
* 2" Ti plates are here and in queue for cutting into swiss-cheese plates.&nbsp; {color:#3300ff}{*}Jerry/Ray{*}{color} have the drawings for 1 plate; Sample plate drawing (easier) should be finished by next week.
* Oatmeal can is about 20% finished.&nbsp; +Will+ be able to CNC cut the threads on it.
* Several pump parts are here and can be load tested for power draw.
* connectors not ordered but {color:#3300ff}{*}Doug{*}{color} thinks they will be here quickly.
* valves not ordered yet
* complete DWSM instrument will be assembled by end of year.
* Building a high-pressure test interface will cost \~$10K.&nbsp; {color:#3300ff}{*}Doug{*}{color} given advice to charge this to ASTEP, but charge may be split among several funding lines.&nbsp; {color:#3300ff}{*}Jim{*}{color} and {color:#3300ff}{*}Chris S{*}{color}. to meet about this.

h3. GUI Development

* &nbsp;Kevin out sick today, but lots of Confluence activity....

h3. Other Items:

* Diver needs and deployment logistics are still be formulated...
* We are doing well on the [calendar (bottom of page)|ESPAPP:28Aug2008]]]></property>
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<property name="body"><![CDATA[Doug will be on vacation July 14-July 28.
Scott will be on vacation July 16-July 22.

h2.

present:  Chris S, Addie, Scott, Doug, Brent, Jim

h3. Instrument Builds

* Scott still to start work on ROV mate-able interface.  Will 'interface' with Chad and Marko.
* Dwarf boards on track for a mid-August delivery.
* Mid-October is the Monterey Ocean Experiment (MOE), where we want to deploy Moe w/ PCR.  Our backup plan will be to deploy the tombstone if the grill is not ready.

* Mid-August we will have SC visitors that will want to run Bruce and Mack very hard for two weeks.  Mostly short DA runs.  issues to deal with:
** Bruce collection clamp issue
** Mack hand.  Scott thinks it may just be a rev of the hand (i.e., widening a hole)

* Must remember that Mack and Bruce are still using back-side puck temp sensors.  Neo has been changed to front, as should these two eventually.

h3. MFB

* Still waiting on encoder boards--due early next week.
* gears still to be modified; should be done today
* syringe mount missing two pieces from El Camino order.  Addie checking with Mike.  We may have one set made in-house so as not to wait.
* Will find two dwarf boards for the grill so not to slow Addie.  One must be Rev. 2, Scott looking around for solution.
* Immediate solution to driving the grill will be to use Linux laptop that Bob Herlien has.  Eventually will move to a more portable solution.
* Jim will email Tony asking for another PCR module
* Brent made offer to help with instant Ruby graphing of PCR module data, if/when Addie gets some downtime.

h3. Software

* Much discussion about freeing up ESPShore space.  2 DVD sets and 1HD backup currently exist. _It was decided that files older than_ {color:#ff0000}{*}{_}July 2006{_}{*}{color} _could be deleted._ Brent and Roman will be the deletors.
* Much discussion about radio link to M0.  Brent has found a private residence that provides beautiful, unobstructed access and has suggested we offer to provide them DSL if we can mount antenna on their house.  Chris S. looking into the legalities and if this would be okay with MBARI.  Stay tuned.

h3. DWSM

* Bell housings at El Camino.  Doug found o-ring problem and has forwarded them a Rev C to work from.
* Swiss Cheese plate will not be finished b/4 vacation.  Maybe EC will make blank and MBARI will do detail work.
* valves not ordered - only a 4-day lead time
* building a fabricated parts list.

h3. Other Items

* ESP running next weeks BBQ.  Jim will organize.  Need 3 cooks/3 cleaners.  Brent has offered a curry rice salad to go with our burgers and famous Costco cookies.]]></property>
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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* October deployment:
** Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs).

h3. Machine Builds

* Puck sensor boards (10 made) have been modified and {color:#0000ff}{*}Scott{*}{color}is still testing on GG in the fridge.&nbsp; Will fit in as fridge schedule opens up.
* Mack giving many problems to SC group, who leave tomorrow.&nbsp; {color:#3300ff}{*}Chris{*}{color} thinks its a PBV calbration problem.&nbsp; Intermittent.&nbsp; Scott will start tackling this on Tuesday.
* Syringe testing:&nbsp; not really time-critical.&nbsp; Will perform after October deployment.&nbsp; {color:#3300ff}{*}Scott{*}{color} also wants to test on syringe frames in the cold.&nbsp; Still waiting on delivery of 10ml CS.
* {color:#3300ff}{*}Dick{*}{color} checking Dwarfs and R-valve boards.

h3. &nbsp;MFB

* Tombstone (TS) has worked in the cold.&nbsp; Now re-doing at ambient to compare.
* There was a never-before-seen error in the driver data from the module;&nbsp; maybe the module burped data that Ruby couldn't handle or it could be a threading issue.&nbsp; Bob Herlien is being contacted about this problem.
* Bracket to hold PCR module on grill will be ready Tues/Weds next week
* All syringe speeds on TS are working with voltage regulator on syringe and rotary valves (not heaters).
* Have noticed the gains on the grill syringe are much different than those on the TS, probably due to plunger/syringe tightness differences.&nbsp; Means Grill uses more power than TS.
* Seal on mixing column still not good.&nbsp; New o-rings ordered, will come in Tuesday.&nbsp; {color:#3300ff}{*}Addie{*}{color} to buy PEEK tubing cutter.
* Stand-Alone power boards are not critical path yet, so {color:#3300ff}{*}Scott{*}{color} will wait until after deployment.
* {color:#3300ff}{*}Addie{*}{color} and {color:#3300ff}{*}Chris P{*}{color}. need to come up with a test plan for the TS/Grill for mounting on a&nbsp; core.
* {color:#3300ff}{*}Addie{*}{color} will let {color:#3300ff}{*}Mike P.*{color} know that we are mounting TS on Neo for October; mike should start the physical mount Sept 9-11.

h3.


h3. Software

* Limit switch code is now working.&nbsp; Small slight tweaking needed, but pretty much finished.
* Mack's brain freeze; stuck doing a single Ruby primitive.&nbsp; We killed process and started again.&nbsp; Will look for it to happen again.
* Upon looking at antenna house,&nbsp; {color:#0000ff}{*}Brent{*}{color} and {color:#3300ff}{*}Wayne{*}{color} are making slight changes to antenna location.&nbsp; We want to 'kit' the installation so there will only be 1 visit.&nbsp; Brent continues to try and setup the router/antenna.&nbsp;

h3. DWSM

* &nbsp;{color:#0000ff}{*}Doug{*}{color} found that bell housing still not finished; next week.&nbsp; Anodizing will use a sodium dichromate seal with no color added to the anodizing.
* much discussion about anodizing to slow galvanic corrosion; Sphere is too large to anodize so perhaps use a polyurethane spray.
* Critical Path for DWSM is the swiss cheese plates.&nbsp; Plans have been given to Ray & Jerry who think they can do it.&nbsp; Must check with them for a timeline.
* Soup can is now a 2-piece Oatmeal can, which we are doing in-house.
* {color:#3300ff}{*}Scott{*}{color} still to order connectors in and out of DWSM housing.
* Doug explained the possible testing procedures of DWSM in his email:{color:#006600}There are two pressure modes and three assembly options.{color}
{color:#006600}&nbsp;{color}
{color:#006600}Running modes are: ASME rated (aka safe to stand next to) and Exclusion (put in pressure test facility and run remotely){color}
{color:#006600}Assembly modes are: 3/8" SS internal screws and open HP motor, 3/8 screws and closed HP motor, or B7 jacket bolts. The HP pump shaft seal has low pressure limit, hence the need for the compensated motor. The jacket bolting needs the complete closed housing assembly, MINK's cables, etc.{color}
&nbsp;
|| || ASME Rated || Exclusion ||
| 3/8 Screws, open HP motor | \~10 psi | \- |
| 3/8 Screws, closed HP motor | 220 psi \\ | 550 psi \\ |
| 7/8 B7 Jacket | 1500 psi | 5885 psi |
{color:#006600}This means that we do need the soup can housing to do any significant development, but that we can run the full cycle (at reduced pressure) before fully terminatingeverything. The soup can is in the machine shop queue along with a lot of other parts that we need.{color}
&nbsp;
* Scott suggested we go ahead and rent a Freezer van to both test the sphere at temp, and use as a pressure test housing for the DWSM.&nbsp; will look into.
* {color:#3300ff}{*}Scott{*}{color} to order connectors that go in and out of DWSM housing.
* Doug to order normal Swageloc SS fittings and test corrosive properties against Ti plate.
* Quote of the day:
** "Nothing on DWSM will be effected by the cold."&nbsp; \--Douglas Pargett 8-28-2008 11:48am ;-)

h3. GUI Development

* &nbsp;Kevin making changes to GUI in time for Oct deployment
* Will be finished by Sept 26.
* Still trying to get an evaluation version of machine state software.

h3. Other Items:

Invited paper to Oceanography is due Sept 15.&nbsp; Chris will need help with some figures.
\\

Project Calendar for Sept/Oct:
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<property name="body"><![CDATA[Our first 'labeled' scintered frits arrived

 *{+}23 April, 2008{+}*.&nbsp; These were 10um frits, labeled 'D'. Specifics of this order:

Job #36366
Disc Dimensions: 0.998 \+0.000/-0.002" OD x 0.062 \+/-0.005" thick
Porous Grade: 10 Micron Grade
No Chamfers
Porous material Chemistry: Titanium Grade 2 per unified
PO# 0810358&nbsp;

These frits did {color:#cc0000}NOT{color} have finished edges, and were 0.057" in thickness, within tolerance specified, but thinner than original frits.
Future orders should specify edging and a lower thickness tolerance to get closer to the 0.062" thickness.
\\

The convention, decided in emails Feb 26, 2008, will be:

0.1, 0.5, 1, 10um frits will be labeled

A, B, C, D respectively.&nbsp;
\\

We have had CE Metallurgical make the 'press' for these so subsequent batches should be less expensive.&nbsp;

*{+}March 26, 2009{+}*

Jobs #38015, 38016, 38017
Disc Dimensions: 0.998 \+0.000/-0.002 OD x 0.063 \+/-0.003" thick&nbsp; (note slightly thicker with narrower tolerance than first order)
PO# 0910403

0.1 um (labeld 'A') $10.25/ea
20.0 um (labeled 'E') $7.55/ea
50.0 um (labeled 'F') $7.55/ea

Ordered 100 of each size.

*+&nbsp;December 30, 2009{+}*

Placed the following order:

Jobs
Disc Dimensions: 0.998 \+0.000/-0.002 OD x 0.063 \+/-0.003" thick
PO

0.2 um (100; labeled '2') $10.25/ea
0.5 um (100; labeled 'B') $10.25/ea
1.0 um (100; labeled 'C') $10.25/ea
10 um (300; labeled 'D') $5.85/ea

{color:#0000ff}Contact{color}:

Chand Eisenmann Metallurgical
258 Spielman Hwy
Burlington, CT&nbsp; 06013

860-675-5000

{color:#0000ff}email:{color}
me@chandeisenmann.com&nbsp; (Mark Eisenmann)]]></property>
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<property name="body"><![CDATA[The radio must be configured one of two ways:

1)&nbsp; As a Point to Point master with FreqKey = 4
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; For use at Santa Cruz with ESPmack

2) As a MultiPoint Master with FreqKey = 2
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; For use at M0 with ESPbruce and ESPneo

After you've plugged in the radio, antenna and power supply...

0)&nbsp; Connect the radio to the laptop's serial port.
1)&nbsp; Power on the laptop
2)&nbsp; Log in as user esp
3)&nbsp; bring up the GUI
&nbsp; $ startx

4)&nbsp; Bring up two terminal windows
5)&nbsp; In one change to the root user
&nbsp; $&nbsp; su

6)&nbsp; In this root window, start picocom to configure the radio

\#&nbsp; picocom&nbsp; \--baud=19200&nbsp; /dev/freewave

7)&nbsp; Toggle the radio's configuration switch
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Configure the radio appropriately:

&nbsp;&nbsp;&nbsp; On the Operation Mode menu select either
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Point-to-Point master for Santa Cruz
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; or
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Multi-Point master for M0

&nbsp;&nbsp; On the Radio Transmission Characteristics menu
&nbsp;&nbsp;&nbsp;&nbsp; Select Freq Key of
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4 for Santa Cruz
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2 for M0

8)&nbsp; Exit radio configuration mode by pressing ESC at its main
configuration menu

You should now see a link on the radio if the other side is up.

9)&nbsp; Exit picocom with the key sequence:

&nbsp;&nbsp;&nbsp; Ctrl-A&nbsp;&nbsp;&nbsp; Ctrl-X

10)&nbsp; Start the appropriate networking stack on the laptop

&nbsp;&nbsp;&nbsp; #&nbsp; ifup&nbsp;&nbsp; ppp0&nbsp;&nbsp;&nbsp;&nbsp; #for Santa Cruz
&nbsp;&nbsp;&nbsp; #&nbsp; ifup&nbsp;&nbsp; sl0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #for M0

11)&nbsp; In the other (esp user) terminal window

&nbsp;&nbsp;&nbsp; $&nbsp; ssh&nbsp; ESPxxx.radio

where xxx is either mack, bruce or neo

This should get you an esp user shell on the desired machine

When you move between mack/bruce and neo, you will need to switch both
the freewave
radio configurations and the laptop networking.&nbsp; Before you can
reconfigure the radio,
&nbsp;you must bring down the laptop's current&nbsp; networkinginterface to it.

12)&nbsp; In the root window:
&nbsp;&nbsp;&nbsp; #&nbsp; ifdown&nbsp; ppp0&nbsp;&nbsp; #if you've been talking to&nbsp; ESPmack.radio
&nbsp;&nbsp;&nbsp; #&nbsp; ifdown sl0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #if you've been chatting to ESPbruce.radio or
ESPneo.radio
Then, go to step 6]]></property>
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<property name="body"><![CDATA[Jim and Chris will be gone next 2-3 weeks.&nbsp;

h2. Plans to be completed by week of June 30:


h3. Tech Transfer

* Finish NEO temperature calibration then give to Science for exercising
* verify boards for MOE and mount/install
* start fluidic buildup
* waiting on several items (pressure sensor, various machining from El Camino)&nbsp;

h3. MFB

* Finishing SCWRRP samples this week
* Yesterday laid out detailed decision-tree on future experiments
* Chris P. to make sure enough MM, P/P, template for uninterrupted runs for next 3 weeks
* Tony fed-ex'd PCR tubing yesterday.&nbsp; Arrived today.
* SPE heater elements had to be sent back to company for thermal-conductive adhesive, which they forgot to apply.

h3. Software

* Communications w/ Bruce are intermittent.&nbsp; Should check buoy for kelp and/or position
* Mack showing large dB loss in its communication.&nbsp; Brent suggests we take off some of coiled cable in roof antenna to give us a few dB more signal.
* Brent to work with Roman to re-structure ESPshare for better file arrangement.
* A newer version of the 'notifier' software will queue both good and bad news and hold in queue until sent.

h3. DWSM

* Doug will finish bell housing designs, have them reviewed internally, and send to El Camino for quote
* Finish designs of mag coupling pressure shrouds.&nbsp; We will manufacture here
* Finish design on swiss cheese plates
* order valves
* high-pressure motor should arrive next week

h3. Other Items

* &nbsp;Chris S. has noticed that during this network deployment, images on Bruce consistently coming in dimmer than Mack, even though both have identical reagents.&nbsp; We believe images were the same before deployment.&nbsp; Scott thinks it could be due to differences in camera electronics due to the cold.
* CDR continuation:&nbsp; DWSM electronics and software CDR will be {color:#ff0000}{*}Weds. July 9{*}{color}.&nbsp; Invitations will be sent to Tom O., Mike Risi, Kevin G. Doug Au, Ed M., Chad K., Paul Mcgill.
* Scott still needs to do preliminary design of ROV mate-able interface and pressure board so plenty of work before CDR.
* Bruce/MACK recover is Monday, June 30.
* RE: newer chips. {color:#3300ff}35{color} of {color:#ff0000}52 dwarf boards{color} will be populated with old controller chip, the remaining boards will have that position left empty should we decide to&nbsp; upgrade

h3.

Congratulations to everybody on a great deployment.&nbsp; We have three working instruments, two in the water for over 2 weeks, and much science data to chew on from this successful engineering effort.]]></property>
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<property name="body"><![CDATA[h5. {color:#3300ff}Thanks to the entire team for making yesterday's deployment...{color}


h5.


h3. Deployment Update

ESP Mack (SC)-\- radio-link weaker than expected.&nbsp; Brent going to do some home tweaking to see if he can get better signal

ESP Bruce (M0)-\- new CTD is not playing well with driver code.&nbsp; Possible solution has been pushed to it. Bob H. and Brent working on other solutions.&nbsp; Gaps in CTD data have no effect on ESP core runs.

ESP NEO (M0)--Linux kernel has frozen for a second time.&nbsp; It seems to take an exception, writes a log of it, try again, log again, and builds 30MB log file.&nbsp; Brent finally got in and restarted Linux.&nbsp; We used 3 pucks; 4 remaining BAC arrays are next up. This may be due to an updated SLP protocol with our old kernel...

&nbsp;Monitoring during this deployment

Chris S. and Brent will get all bad news; Chris email, Brent email and phone text.&nbsp; Cheri will receive bad news text messages as backup.

Chris P. will receive all messages via email, with the chore of looking for procedures that do not occur (not necessarily bad news).
\\

Pickup date is Monday, Oct 27 with Shanna Rae.&nbsp; Will drive to SC, got get 'em, return to Moss landing.

h3. Machine Builds

* Dwarf Boards:
** boards that failed inspection (~30%) will&nbsp; be resoldered when Dick returns from vacation (Oct 20), and retested.
** Wayne writing a 'theory of operation' for dwarf and R-valve boards and will meet with Brent to get an overview, and bounce ideas.
* Cheri: will provide a build schedule for Moe. This needed so we can plan the McLane visit(s) during the build of the next two cores.
* By the end of next week, Addie will have a total parts order for ALL remaining MFB's.&nbsp; We'll submit to a shop in San Jose as El Camino is too busy.&nbsp; This will allow a visit from Mclane for MFB construction in early December.
* USB Camera: new camera's are not backward (slower speed) compatible w/ our boards
** We have a 2-stage decision:&nbsp;
*** talk to company about fixing their camera firmware to be truly backward compatible-Brent will try to get to them next week.
*** put something b/w the camera and our board that will allow USB 2.0 to work with our slower boards.&nbsp; These are commercially available.

h3. MFB


h3. Software


h3. DWSM

* Tapemation machinist on vacation.&nbsp; No sphere work performed since last week&nbsp;&nbsp;&nbsp;
* Ray having difficulties with swiss cheese plate: our CNC not quite beefy enough; he and Doug working on a solution
h6.

h3. GUI Development


h3. Other Items:]]></property>
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<property name="body"><![CDATA[h3. Deployment Update

* All three instrument working well.&nbsp; Problem with Neo's radio was that it was running on low power.&nbsp; Trip to mooring allowed this to change.&nbsp; Santa Cruz radio link was spotty; Brent thinks that the mooring is 100 yards too far east forcing signal to traverse lots of land.&nbsp; A minor tweak of his roof antenna has made transfer speeds acceptable.
* Neo has had 1 error; elevator retry while moving pucks; doesn't look serious.
* Message rules need to be reviewed; phone emails of bad news are not getting sent.&nbsp; Scott and Brent to work on this.

h3. Machine Builds

* MOE:&nbsp; temperature mounts made and now on
* elbow and harmonic drive still problematic.&nbsp; Many hours by many people spent to get drive aligned but no luck.&nbsp; Going to plan B:
** order 2-axle (pre-aligned) harmonic drive and redesign mount on arm
** use GG's arm to finish build and calibrating of Moe.&nbsp; Cheri estimates 2 weeks and it will be ready to hand to science.
* Cheri working on BOM for the two ASTEP II instruments to be built in 2009.
* El Camino has delivered a small number of parts for the next two units

h3. MFB

* Parts list for 3 ASTEP II MFB's and remaining parts for current 7 MFB's will be finished early next week.&nbsp; Plan is to send jobs to a Santa Cruz shop since El Camino is overbooked.
\\

h3. Software

* Starlight Xpress, our camera manufacturer can still get old USB boards, but upon recalculation, we may not need them for 2009.&nbsp; Currently we have 4 USB 1.1 cameras:&nbsp; Doucette, Scholin lab, spare, and GG's. We could purchase and trade 2 newer cameras for Doucette and Scholin lab, and have 4 older cameras available.&nbsp; Would still like a price for Starlight to make the old ones, but now no rush.
* Brent arranged a visit from a board manufacturer with ties to LabView.&nbsp; Invited interested parties.
* h6. &nbsp;DWARF ISSUES:

** Wayne has found you can take a good board, but when trying to clone bits from it, we can't identify the processor.&nbsp; Much discussion on why this may be; perhaps blown fuse?
** Writing of Dwarf Novella;&nbsp; {color:#3300ff}{*}Brent & Wayne to meet Monday 2-4pm{*}{color} to discuss this.
** Wayne building a Verilog motion-control test bench for Scott.
** Cloning of Bufflehead:&nbsp; {color:#ff0000}{*}Friday, 1:00pm start of clone{*}{color}.

h3. DWSM


h5. Sphere

Doug made Tapemation visit on Tuesday:
** Sphere bottom looks good.&nbsp; Lathing finished, now onto mill; should be finished ~ 2 weeks.
** Top still an issue.&nbsp; Doug re-did drawings to try and adjust to the poor casting.&nbsp; Top will need minor machining (lift points, and thru-holes to connect to bottom)
** Pictures of these are in project Library.&nbsp; Check out {color:#990066}*/projectlibrary/ESP/DWSM/4k DWSM/4k Sphere Pictures/4k Sphere machining{*}{color}

h5. DWSM

* &nbsp;Will be built in Bldg. B lab
* Must build a test-rig for filtering oil
* Bulkhead plates (swiss cheese) have finished face-machining.&nbsp; Now doing sides of plates.&nbsp; Looks like Ray will finish before he goes on vacation.
* Doug ready for Dwarf/host/sleepy combo to start testing subassemblies.
* Syntactic foam to arrive in January.&nbsp; Currently enough foam for 12 batteries, which is out contingent weight (if stuff is heavier than calculated, we will have to remove some batteries, lessening deployment time.)
* Preliminary elevator idea has been vetted with Lobos crew.&nbsp; Preliminary dimensions and weights will work.

h3. GUI Development


h3. Other Items:]]></property>
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<property name="body"><![CDATA[On all ESPs there have been these
easier to use power control command varients for some time:

Power.dwarf :on
Power.dwarf :off
Power.raw :on
Power.raw :off
Power.camera :on
Power.camera :off

Power.camera returns true if the camera is powered
Power.dwarf returns true if the dwarves are powered
Power.raw returnes true if raw 12V is enabled

On ESPneo, shutdowns will be deferred until all "background"
threads threads have terminated.&nbsp; ESP.shutdown or Sleep.shutdown
will produce a log message to this effect.
The message indicates which background threads are causing
shutdown to be deferred.

You can always get a list of the background threads with:

Sleep.background

If you want to force a shutdown anyway, here's how:

Sleep.shutdown\!

To power up the ESP after a shutdown:

ESP.wakeup
or
&nbsp;Sleep.wakeup
\#cancels any pending shutdown.
\#does nothing if the ESP is already powered.
\#otherwise, powers up and readies all but the MFB

If you're impatient:

Sleep.restart\!&nbsp;&nbsp; #forces a power cycle, reconfigures dwarves, but does
not home


ESPs other than neo never defer shutdowns and do not implement
Sleep.shutdown\! or Sleep.restart\!

\-\-
&nbsp;Brent Roman&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; MBARI
&nbsp;Software Engineer&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Tel: (831) 775-1808
&nbsp;7700 Sandholdt Road,&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Moss Landing, CA 95039
&nbsp;mailto:brent@mbari.org&nbsp; http://www.mbari.org/~brent]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Birch, Everlove, Jensen, Pargett, Harris, Roman, Gomes
Absent: Scholin

h3. Tech Transfer

* Cheri has started putting orders in for CMORE core we're building

* MACK doing first post-rebagging runs.  QCing reagents today.  If good, we'll load with pucks

* BRUCE: will start today with qualifying assay runs.  Going in cold {color:#ff0000}MAY 5{color}.  Will use GG's lid.

* NEO: has all new valves. Positioning needs verification.
* hand needs finishing, swapping, and calibration
* Neo goes in cold room {color:#cc0000}MAY 12{color}.  Will use new lid.

h3. Deployment

* Bail is being modified with weld so divers don't need to strap it on launch/recovery
* ISUS needs refurbishing-has been left with Luke who will do it early next week
* Monday Scott to work with Jose to refurbish battery pack (will be using a new one); for the 19 day deployemnt we used \~1/2 the battery pack.  Probably get 6 weeks from full pack.
* Mike notified about diver needs
* Zephyr on Thursday @ 7am, leave @ 8am.&nbsp; Deployment team still to be determined.

h3. MFB

* New block from LLNL arrived this week.  Several scripting changes have been implemented which have helped stop killing our probe label.  We have run slugs on old and new blocks, and gotten very nice endpoint results.  Gels still to be run.

* Backgrounds on the two optical channels still are high (with water, 1630-1700 depending on channel).

* Need to find new heater vendor; Addie working on this

* Solid Phase extraction columns.  Order approved, but building it becoming a problem.  Addie trying to track down our original manufacturer.

* Must check with Mike Parker to see how his tombstone design on Moe is coming along.

h3. Software

* NEO - firmware and Linux host needs updating
* MACK - needs Ruby with email notification.  Brent will change and then exercise it through some mini-missions

h3. Sphere and 4K DWSMS

\*Must pull together a deployment plan for the Lobos and DWSM as there are still big holes in the DWSM plan.
* Mtg scheduled for April 30.
* Scott has gotten one of the brushed motors to work off the dwarf (GOOD NEWS) so we can drive high power things directly from dwarfs.  Discussion to these benefits/logistics to be taken offline.

h3. GUI Development

* The deployment GUI has been used for two deployments, and Kevin continues to get feedback and tweak it with each subsequent deployment.]]></property>
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<property name="body"><![CDATA[\\
{tip:title=Who we purchased the D-ESP van from:}

h2. American Portable Storage

Purchased Feb, 2009
Oakland, CA
1-800-838-4006; &nbsp;(Ken)

Purchased 20' van, 220V Single Phase with 3hp refrigeration system, good from \-10 to 55F.&nbsp; SS sides, aluminum floor.
Michael McCurley--his quote is [here|^MBARI Quote.doc].
Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].
PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)
{tip}
{tip:title=Who we purchased the Reefer Shipping Van from:}

h2. Cold Box  (I believe this was a spin-off of APS above)

Purchased 20' reefer van July, 2011
Oakland, CA
1-800-595-0601; (Mario Leon)
Quote is [here|^Shipping Van quote.pdf]
PO is [here|^Shipping Van PO.pdf]

Internal dimensions:  86" high, 89.5" wide, 212" long

{tip}]]></property>
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<property name="body"><![CDATA[h5. {color:#3300ff}Thanks to Scott, Brent, Roman, and Cheri for the long hours last night bringing Neo and Mack back to life...{color}


h5.


h3. Deployment Update

* MOB Tuesday PM, depart Weds morning 06:30.&nbsp; Crew will be Chris S., Roman, Scott, divers: Lonny & Mike.&nbsp; Crane operator Luis, with x-tra pay for childcare/OT.
* Will deploy one @ MO, travel to SC, then back to M0 (allows 1 hr b/w each dive for divers)
* In water will fire off full-phase.&nbsp; Then rest and start on 11th.
* Moorings:&nbsp; lots of little things still to do, but coming along nicely.
* h4. The Plan:

** Mack and Bruce will be canned tomorrow (Friday).&nbsp; Bruce will be moved to it's mooring in preparation for radio testing.
** Brent will radio test Mack Friday.
** Saturday, Chris P will load PCR reagents on Neo.&nbsp; Then start a 24hr run lat Sat, making sure to do a full MFB with BAC run.&nbsp; This will confirm all reagents are good.&nbsp; {color:#cc0000}At start of this run will note power on Watts-up meter so we can get a power usage estimate for a full run{color}.
** Neo gets canned Monday
** Dual radio testing for Neo/Bruce Monday.

h3. Machine Builds

* Dwarf Boards:
** Dick soon to go on 2 wk vacation
** All boards tested.&nbsp; 6 R-valves fail.&nbsp; Failures came on motor tests.&nbsp; Could be Xylinx solder joints.
** Wayne writing a 'theory of operation' for dwarf and R-valve boards
* Issues with cores:
** Mack: replaced a dwarf board yesterday when it was acting unreliable.&nbsp; First board to go bad in long while.
** NEO:&nbsp; Brent fixed jittery Sample syringe brought about by too slow a minimum speed for integrator to adjust to. This change may need to be carried to all cores.
**** Brent noticed hand could not extend all the way.&nbsp; May be a calibration/config issue; will work with Scott on this
**** Software:&nbsp; issue with getting emails outside our firewall; Brent chewing on a fix for this.
*** Chris wants to run short IPC and SAR 11 to see if column is working.&nbsp; After that, run some negatives to show it's clean.&nbsp; then fire off a full SHA.

h3. MFB

* Grill progress stalled until Mike gets freed up.&nbsp; Addie asked to put in formal requests for work to get into que.
* New MFB user's manual will be on Confluence Friday or Monday.
* New LLNL module not tested; waiting on SPE heater block from Mike

h3. Software

* New CTD's have different firmware.&nbsp; Nontrivial.
* CS syringe on NEO has been changed
* Bruce--got stuck last night.&nbsp; Anytime tried to move a syringe or valve it hangs.&nbsp; It waits for a thread that's already dead.
* Mack--PS and clamp got corrupted (overcurrent errors).&nbsp; Sent out a 'recover' and it fixed it.
* Can't seem to FTP into shore station from his house
* Radio tests worked well, but while one file is uploading, link is monopolized (we can't talk to the other machines)
* Will give radio's to Jose
* Home syringe has been renamed.
* Firmware code still not frozen until Brent fixes: 1.&nbsp; Recover from hang due to dead thread, 2. Link protocols fixed, 3. CTD changes made

h3. DWSM

* Sphere bottom (2nd casting) is finished w/ rough out; needs finish work and ports milled
* Sphere top (1st casting) won't make shape, but machining adjustments will make it acceptable (or we'll de-rate it)
* Should be finished in 2-4 weeks
* Bulk-heads (swiss cheese plates) are in the mill and being processed.
* Doug soon to deliver large PO for Pressure transfer barrier (accumulator) for $6K
* h6. Elevator ideas:

** will have roughly 6'x6'x8' size.&nbsp; Lobos crew thinks size will be fine
** Doug believes 4 leg will be more stable than 3
** Foam pack findings:
*** 40lb/ft^3 will be $16K; 28lb/ft^3 will be $20K; Glass spheres will be $10K but much risk
*** will go with 28lb/ft^3; they say \~January delivery.&nbsp; Buying in brick format so useful for others after ESP project ends.
** Much brainstorming about elevator design, working at angles, how to counteract uneven surfaces, etc.

h3. GUI Development

* &nbsp;Kevin working with Chris Preston on the new 'killer' mission planning app; Chris having trouble running on her home machine
* data management software should be finished tomorrow.

h3. Other Items:

* Doug provided a 2009 deployment breakdown.&nbsp; Chris, Jim, Doug will discuss off-line before approaching Grech about schedule.]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15-18, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;

*Jun 6, 2017*

Rich Walsh of SCRIPPS went to buoy and swapped the non-working MELO with a newer one that we had sent down.&nbsp; We are now getting hourly (correct) positions.

*Sept 6, 2017*

Final recovery of Waldo.

h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 27\- May 8, 2017*

This was part of a 5-vehicle launch (Tethys, Daphne, Aku w/ ESP Honu, Ahi, Opah).&nbsp; Gabe Foreman arrived from UH to help with piloting.&nbsp; Adam Jones helped launch Aku and Opah.

Ran multiple simulation to test the mission.

On Weds, May 3, tried first 'real' concurrent sampling.&nbsp; Cartridge 1 threw an alignment error--could not push on plunge valve.&nbsp; We labeled that cartridge 'wet' and moved to cartridge 2.&nbsp; But this notification not written to file, and was lost when power was cycled.&nbsp; Thus, we thought we were onto cartridge #2, but in reality were on #1 (which started working....).&nbsp; Sampling was as follows:

&nbsp;All cartridges started filtering at 60m depth while vehicle ascended to surface, where filtering stopped.&nbsp; WF took CTD casts in the same area at same time.&nbsp; Kevan took 2L each from each of these bottles: 60m, 40m, 20m, 10m, surface and mixed the 10L in a carboy.&nbsp; From that carboy, he sampled 1L through a cartridge on tackle-box, and 1L (x3) on peristaltic.&nbsp; Sample #2 had 1L (x3) through the tacklebox cartridge.&nbsp; Francisco took 1L from each of those depths and peristaltic filtered.

&nbsp;Because of the cartridge number mix-up, Honu returned with a dry #5 cartridge, which we ran as a negative control in the lab.&nbsp; Investigation of the alignment issues is ongoing.
\\

h3. Summary of 3G flights to this point (Dec 2017):

{panel}
*Nov* {color:#0000ff}2014{color} &nbsp;
Very first 3G flight.&nbsp; Makai with one Archive cartridge.&nbsp; Mission lasted \~3 days.
\_____________________\_
*July* {color:#0000ff}2015{color} &nbsp;
First 5-cartridge flight on Makai.&nbsp; All Archive.&nbsp; Cartridge 1 toroid valve stuck in bypass mode, thus recovered only 4 sample filters.&nbsp; All collected <20m deep.

*Dec* {color:#0000ff}2015{color} &nbsp;
First 4 & 1 (archive/LnG) flight on Makai.&nbsp; Many vehicle errors.&nbsp; No stratification so difficult to find any 'features'.&nbsp; Acquired 2 archives and 1 LnG.&nbsp; rough weather recovery.&nbsp; I don't have actual collection depths for these three samples.
\_____________________\_
*Feb* {color:#0000ff}2016{color} &nbsp;
Repeat Dec flight.&nbsp; 1 LnG fired first, then 4 Archives on Makai.&nbsp; Samples taken at 8.7m, 12.7m, 13m, 27m, and 27m.

*Dec* {color:#0000ff}2016{color} &nbsp;
Depth testing with Honu in Makai.&nbsp; 5 archival cartridges.&nbsp; Fired at chl max (~14m), 50m, and 100m.&nbsp; 200m cartridge started, but vehicle cut ESP power before finished.&nbsp; 300m sample had carousel alignment issue and did not complete.&nbsp; 3 of 5 samples preserved.
\_____________________\_
*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; meet with R/V Shimada (CALCOFI ship).&nbsp; Difficulties with water in payload section and rough recovery.&nbsp; Three filters recovered (chl-max to compare to Shimada's, and two at 10m)

*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; CANON cruise and WF rendezvous.&nbsp; Alignment problem had us bypass (so we thought) cartridge #1.&nbsp; Four archives collected, two a smear from 40m to surface, two from 60m to surface.&nbsp; These are matched to ship samples Kevan collected.
\_____________________\_

*Dec* {color:#0000ff}2017{color} &nbsp;
First 60 cartridge-archival mission. Koa on Makai; Deployed Dec 12, recovered Dec 19.&nbsp; Toroid valve motor did not function.&nbsp; No field samples collected.&nbsp; First try and 5 'blocks' of behavior.&nbsp;&nbsp;

\_____________________\_

Overall, we have 21 archival filters that correctly filtered and preserved samples; two LnG samples were collected (were both run through SPR on the vehicle?)
{panel}

h4. {color:#ff00cc}Makai flight w ESP-Koa and 60 Archive Cartridges{color}

*Dec 12 - 19, 2017*

We decided to generate 5 'blocks' of behavior (below) each testing a certain collection scheme, with replicates.&nbsp; Combined samples for Ed with samples for eDNA work.

Out of 60 cartridges, 15 are controls (9 pre-experiment + 6 post-experiment); 45 will be fired offshore.
The 45 field samples are divided into 5 blocks, each block containing 9 samples.
In each 9-sample block, firings are in triplicate bursts: 1, 2, 3 in one continuous burst; then 4, 5, 6; and then 7, 8, 9.

Scientists and engineers will jointly select appropriate sampling locations in consideration of oceanographic features as well as LRAUV operation safety.

Block 1 (Bathymetry alert due to deep sampling):
Mission files:
chlpeak_sampling_InAboveBelow.xml, in donut mode.
depth_sequence_sampling.xml
First, vehicle transits to M1-northeast: 36.760, \-122.012
Then, kick off mission, setting waypoint to M1. Vehicle will do an horizontal search for high chl between M1-northeast \[36.760, \-122.012\] and M1 \[36.750, \-122.022\]; set the hi-chl spot as the sampling location; run a cylinder around the sampling location
Run chlpeak_sampling_InAboveBelow.xml:
3 samples at vertical chl peak depth
Then, run depth_sequence_sampling.xml:
3 samples at 100m depth
3 samples at 250m depth
Total: 9 samples, \~15 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time).

Block 2 (Bathymetry alert due to deep sampling):
Mission file: smear_sampling.xml, in donut mode, on the first 3 samples.
Mission file: depth_sequence_sampling.xml, in donut mode, on the remaining 6 samples.
3 samples smearing between 5m and 100m depths
3 samples at 100m depth
3 samples at 5m depth
Total: 9 samples, \~14 hours (presuming 1hr filtration time + 0.5hr processing time for each sample)

Block 3:
Mission file: isotherm_sampling.xml, in donut mode.
Initial horizontal search for high chl in local area; set the hi-chl spot as the sampling location; run a cylinder around sampling location
3 samples at the temperature corresponding to the vertical chl peak.
3 samples at chlpeak temp - deltaT1
3 samples at chlpeak temp + deltaT2
Total: 9 samples, \~15 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time).

Block 4:
Mission file: chlpeak_sampling_InAboveBelow.xml.xml, in drift mode.
Initial horizontal search for high chl in local area; set the hi-chl spot as the sampling location; run a cylinder around sampling location
3 samples at chl peak depth
Vertical perturbation to reacquire chl peak
3 samples at chl peak depth
Vertical perturbation to reacquire chl peak
3 samples at chl peak depth
Total: 9 samples, \~16 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time + vertical perturbation time).

Block 5:
Mission file: depth_sequence_sampling.xml, in donut mode
Scientists determine a horizontal feature, and set a certain depth for sampling
3 samples at the set depth on one side of feature
3 samples at same depth in feature
3 samples at same depth on other side of feature
Total: 9 samples, \~16 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + transit time)

Vehicle recovered Dec 19, and discovered pulled wire on toroid valve.&nbsp; Toroid pins never moved, so each sampling event pumped through ring (thus the constancy in filtering times).&nbsp; All filters were preserved with RNALater, but none had any biomass.&nbsp; Severe disappointment.&nbsp; Next flight will be late January 2018.]]></property>
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Attend: Everlove, Harris, Jensen, Roman, Pargett

We met and Scott took notes since I couldn't get into the Wiki until just now.]]></property>
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&nbsp;
Instrument Level
|| || Control Loops&nbsp; || || Inputs \\ || Outputs || Torque/Force \\ || Speed range \\ || Accuracy \\ || Precision \\ || ||
| 1A \\ | Sampling Pump motor A \\ | | \\ | | | | | | |
| 1B | Sampling Pump motor B\\ | | \\ | | | | | | |
| 2 | Spool Valve Actuator \\ | | | | | | | | |
| 3 | Cylinder Rotate \\ | | | | | | | | |
| 4 | Cartridge Actuator Alignment \\ | | | | | | | | |
| 5 | Cartridge Actuator 1 \\ | | | | | | | | |
| 6 | Cartridge Actuator 2 | | | | | | | | |
| 7 | Cartridge Actuator 3 | | | | | | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | | | | | | |
| 9 | Cartridge Reagent Valve \\ | | | | | | | | |
| 10 | A/M Clamp \\ | | | | | | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | | | | | | |
| 12 | A/M Hand-off Syringe \\ | | | | | | | | |
| 13 \\ | Cylinder Align/Lock \\ | | | | | | | | |
| | | | | | | | | | |

|| || Discrete Actions || || \\ || Outputs || || || || || ||
| 1 \\ | Intake Select 1 \\ | | | | | | | | |
| 2 | Intake Select 2 \\ | | | | | | | | |
| 3 | Bulkhead valve (intake) \\ | | | | | | | | |
| 4 | Bulkhead valve (exhaust) | | | | | | | | |
| 5 | -Cartridge Valve Actuator 1- \\ | | | | | | | | |
| 6 | -Cylinder latch- \\ | | | | | | | | |
| 7 | A/M Valve 1 \\ | | | | | | | | |
| 8 | A/M Valve 2 \\ | | | | | | | | |
| 9 | A/M Valve 3 | | | | | | | | |
| 10 | A/M Valve 4 | | | | | | | | |
| 11 | A/M Clamp \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |

|| || Raw Input \\ || || Range \\ || \\ || || || || || ||
| 1 \\ | ABS Pressure intake \\ | \\ | 0-500psia \\ | | | | | | |
| 2 | ABS Pressure exhaust \\ | \\ | 0-500psia \\ | | | | | | |
| 3 | intake/exhaust pressure differential \\ | | | | | | | | |
| 4 | \\ | | | | | | | | |
| 5 | \\ | | | | | | | | |
| 6 | \\ | | | | | | | | |
| 7 | \\ | | | | | | | | |
| 8 | \\ | | | | | | | | |
| 9 | \\ | | | | | | | | |
| 10 | \\ | | | | | | | | |
| 11 | \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |
Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
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<property name="body"><![CDATA[Present:&nbsp; Allison, Chris P, Elif, Roman, Doug P., Vanessa, John R, Jim

h3. Items:

1.&nbsp; Just discovered that McLane Pucks do not fit in puck-puller, and some have burrs.&nbsp; Doug has done cursory inspection and they seem to be at the limit of tolerance specifications.&nbsp; Will quarantine and inspect after we get Gordon on MARS.

2.&nbsp; Printer.&nbsp; Roman to try running printer without HEPA filter.&nbsp; Perkin-Elmer doesn't know what to suggest to do, even if they send someone.&nbsp; We are losing this one...

3.&nbsp; Gordon.&nbsp; in the middle of core/mfb testing.&nbsp; Some issues with RNALater being left in WCR pucks.&nbsp; Will do some testing on NEO before implementing in Gordon.&nbsp; Tonight to run BAC SHA MFB phase (low pressure).

3.&nbsp; Vanessa leaves saturday.&nbsp; She's running her MFB standards again and they are&nbsp; looking as good or better than pre-deployment\!

4.&nbsp; John R. reports that the LMO submission has gotten very favorable reviews.&nbsp; He will address and resubmit but things looking good for publication. \\

Jim to tour Fred Byus (RADM, retired, formerly Oceanographer of Navy), currently VP for marine market segment for Battelle in the ESP lab. ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris S., Doug, Brent, Jim, Roman

Absent: Chris P., Scott, Cheri, Wayne, Kevin
\\

h2. &nbsp;Issues:

1.  Benthos Box:&nbsp; Unknown if it has arrived as of today.

2. &nbsp; Brent has been working with Cheri who is at McLane getting 'Mira' up and running.&nbsp; Various issues (pressure differential and syringe mov't, change time to EST) are causing problems.&nbsp; Brent is helping track down and solve.

3.&nbsp; Must discuss the new HP laptops; are they working for everyone, and do we provide them with the MFB's?&nbsp; {color:#ff0000}This is a future to-do item{color}.


h2. Methane cruise

1.&nbsp; Pressure interface has been cleaned and will be tested today.

2.&nbsp; Doug close to installing new bulkhead valves; they needed slight modification, which machine shop has finished.

3.&nbsp; Noted that Chris P. has much on her these next two weeks getting Gordon ready.&nbsp; We will revise her plan for MFB training during the week of the 24th--perhaps bring Julie in to help to give Chris more bandwidth to work on Gordon issues.

4.&nbsp; ESP Van will be temp controlled to ~ 65F starting May 24.

5.&nbsp; Brent wants to meet with Chris P. and finalize the 'day-phase' procedures and figure puck usage.


h2. M0 Flip

1.&nbsp; 22m E/M cable is painted and we re looking for spreadsheet with float locations.

2.&nbsp; batteries on mooring; bungees finished today; tomorrow Roman will finish mooring

3.&nbsp; Checked with Jose, and he'll get E/M cable 'ohmed' out after getting specs from Scott this PM.

4.&nbsp; Roman will be printing arrays all weekend.

5.&nbsp; Chris P and Brent discovered a serious bug in the SH2 protocols that effects all machines, that does not allow recovery if error occurs in a certain specified window.&nbsp; Decision has been made to add a patch to Bruce, Mack, Moe, and NEO.\\ \\]]></property>
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<property name="body"><![CDATA[Present:&nbsp;&nbsp; Chris P., Roman, Julie, John, Jim

Absent: Bill U., Chris S.


{color:#3300ff}1. Updates:{color}\\
* {color:#3300ff}Array printing update{color}
** Computer that controls printer is replaced and is running.&nbsp; Nilo coming in Saturday to print arrays.

* {color:#3300ff}NEO deployment next week{color}
** Roman to paint cable tomorrow (Wed).&nbsp; Clean bungees, mooring assembly still to do.&nbsp;
** Will use Gordon's CTD to test the new memory wipe method we will try on the deployment next week.
** Must ohm-out the cable.
** Julie saw a problem where carousel lost it's position; Brent and Scott both looked at and could find nothing wrong.&nbsp; Restarted.&nbsp; Standard PCR curves looking good.
** &nbsp;Moe PCR's seem inhibited; Julie going to sample less (< 1L) to see if that brings up the signal.&nbsp; Chris P suggested altering pressure differential to try less hard to get 1L if water is mucky.&nbsp; Much discussion about how to deal with PCR inhibition.
** Puck cleaning continues for this deployment and for Gordon.&nbsp; Arrays won't be ready until after weekend, so canning not until Monday
** Melancon to come out Monday AM for filming.
** puck cleaning continues thanks to Julie and Chris P.
** getting MSDS on the anti-fouling paint from Patrick Whaling.&nbsp; No one really seems to know how toxic, so we will become the informed ones.
** ERROR TRACKING:&nbsp; Kevin has nifty way of culling log files of all errors during a deployment.&nbsp; It does not catch the email traffic or solutions on how the errors occurred, but noting the failures is a start in our journey towards deployment experts.

* {color:#3300ff}MFB training{color}
** Chris P has readied MFB10; MFB2 will also be used in training, but needs PCR module replaced.&nbsp; Cheri tasked with that when she returns from McLane.
** Looks like 6 people coming for June 7 MFB training.&nbsp; 2 Stanford, 2 SCCWRP, 1 MLM, 1 Cawthron..&nbsp; Others may float in and out during the week.&nbsp; Must figure out WHERE this training will occur.

* {color:#0000ff}D-ESP preparations--Gordon{color}
** Chris P has started making reagents.&nbsp; PCR reagents from Patty to arrive today.
** Must check with Brent t see that Gordon has correct config file.
** Wed PM/Thurs AM will have reagents on Gordon
** Core testing to start next Weds.

* {color:#0000ff}Bruce forensics{color}
** {color:#000000}Waste container does NOT appear to be full.&nbsp; No smoking gun on error.&nbsp; When we pulled from air1, it behaved like we were sucking fluid.&nbsp; Worked well from air2, but would not work from air1, so we aborted mission.&nbsp; Now it's working ;&nbsp; does not seem to be a 'tilt' issue...{color}

* {color:#0000ff}John R. Paper progress{color}
** Writing continues.
** Possible places of submission:&nbsp; Harmuful Algae, L+O Methods, Marine Biology Progress Series

* {color:#3300ff}Chris P. paper progress{color}
** {color:#000000}nothing this week.&nbsp; Too busy deployment/training/Gordon preparations.{color}

* {color:#0000ff}BioSpace deployment in October{color}
** John R. has a tube of rhodamine that will be in water to track current movements.&nbsp; We need to test in ESP at anticipated dilutions to see it's effect on our chemistry and on the PCR module.&nbsp; Chris P. will look into emission spectra\\]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim B., Chris P, Roman M., Wayne R., Cheri E., Brent R., Chris S., Scott J., Doug P.

Absent:&nbsp; Cheri E.

h2. &nbsp;Issues:

1.  Benthos Box:&nbsp; Supposedly being shipped today.&nbsp; Should arrive next week.&nbsp; Much testing needs to be done with it and acoustic release, as well as hull transducers on the flyer.&nbsp; Many questions still to answer related to using the acoustic modem on the Flyer.

2.&nbsp; Light seal issues on current cores was not discussed.

h2. Methane cruise

1.&nbsp; Much discussion over puck make-up necessary for this mission and pre-mission testing.&nbsp; [Here|^Puck usage plan for Methane Mound cruise.doc|puck usage plan] is plan as of 13 May 2010.
\\

2.&nbsp; Discussion of schedule once we arrive in LA.&nbsp; Some issues with sharing our van, particularly when we need to run a 'dock' QC before loading on the ship.&nbsp; This issue has been resolved with Theresa.

3.&nbsp; ISUS.&nbsp; Will we use a deep one?&nbsp; Discussion with Bill Ussler has resulted in a negative to that question.&nbsp; Better science may be obtained by collecting water around ESP and running through his GC.

4.&nbsp; Girguis to be called and delivery date confirmed of ISMS and is being shipped to arrive May 19th.&nbsp; Peter changing a turbo  pump, and we need to make wiring harness.&nbsp; mounting brackets already  finished.&nbsp; Scott has cabling which needs potting.

5.&nbsp; Gas canisters.&nbsp; will check to see if we can pre-load on WF.

6.&nbsp; Doug P created extensive list of to-do items.


h2. M0 Flip

1.&nbsp; Need support engineering help to prep the next 15m of E/M cable  for the 25th deployment. Paint and replace floats.

2.&nbsp; Melancon would like to film the canning of NEO and go on the  cruise on Tuesday.]]></property>
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<property name="body"><![CDATA[Present: Jim, Scott, Doug, Bruce K., Roman, Brent, Chris P

Absent: Chris S., Julie, John R.

h3. Issues:

* Much Discussion on schedule of Gordon and D-ESP Prep.&nbsp; Current calendar is [MARS 2010 Calendar|^MARS 2010 calendar v2.pdf].

h6.

* Jose working on 48V switch-over for ISMS integration.&nbsp; Must check with him to see what instructions he was left from Scott.
* Need to call Pete about his ISMS plans.
* Brent working rest of year on integration of newer version of Ruby.
* Also wants to develop .JPEG thumbnails, that could be easily sent over Iridium.&nbsp; This has it's drawbacks, as they can't be analyzed, but otherwise 70MB/30-day deployment is too costly using Iridium.
* Roman to work on array printer.&nbsp; We need BAC arrays.
* The new CTD sensor has an Oxygen sensor; means we need to tweak the new driver.&nbsp; Brent working on this.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris S., Chris P., Roman, Julie, John, Jim

Absent: Bill U.

{color:#3300ff}1. Updates:{color}\\
* {color:#3300ff}Array printing update{color}
** computer died this weekend.&nbsp; New (old) one is coming today or tomorrow.&nbsp; Perkin-Elmer sending tech to set it up and load driver but they will not help re-calibrate tips if that needed.&nbsp; Very disappointed with service they have provided for the price we've paid.&nbsp;
** We are out of BAC arrays; these are first priority for Roman.&nbsp; There is also much work to recalibrate machine and re-create puck maps.

* {color:#3300ff}Cheri headed to McLane on Sunday for the week.{color}
** She will take 2 SH1, 1 LAF, 1WCR pucks and filters/supports.&nbsp; Roman will help get those together.

* {color:#3300ff}NEO deployment next week{color}
** (correct) reagents loading today.
** ball screw has been replaced.
** will hot-swap CTD on ship, so older CTD with current working driver will be in use.&nbsp; Bob Herlien can write new driver, but not until August.
** Pressure sign inversion still to be fixed.&nbsp; Email sent to Scott to band-aid by placing different resistor on sensor board.
** discussion about how ISUS is powered.&nbsp; Currently runs once every 20 minutes and thus 1 battery will take it 6 months.&nbsp; If sampling more frequently, we must upload more often and batteries discharge and memory fills.&nbsp; Must talk to Brent if sampling frequency to be increased.

* {color:#3300ff}Check-out/fix broken PCR modules{color}
** We will assemble data on the malfunctioning of each module and submit to John D @ LLNL and ask for help.&nbsp; This will occur after the flip.

* {color:#3300ff}Bruce/Mack{color}
** Mack had an extra puck in one tube, due to the machine being stopped when the hand was gripping over the carousel.&nbsp; We were lucky it fell into tube 5 so it could continue a HAB run from tube 4.
** Bruce to be opened tomorrow.&nbsp;
** We will appeal to Support Engineering to help in mooring cleaning and preparation.

* {color:#0000ff}John R. Paper progress{color}
** John has sifted through contextual data and skimmed the nuggets of interpretability.&nbsp; Seems like a very nice story is emerging.&nbsp; He will send figures and outline draft of paper this week.

* {color:#3300ff}Chris P. paper progress{color}
** Chris continues writing and gave review of the figures she's settled on.
** still looking at submission to PNAS or Applied Env. Micro.

* {color:#3300ff}Methane Mound Cruise{color}
** Much discussion on the timeline of the cruise and when things needed to be done.&nbsp; Chris P. had valuable input into when she could assist.&nbsp; The schedule still is somewhat flexible.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Brent, Scott, Doug, Chris P, Elif, Julie, Jim

Absent:&nbsp; Chris S., Bill U., John R. Roman

Items:\\

1.&nbsp; ISMS slated to arrive next Tuesday (Nov 9).
2.&nbsp; Driver tweak for new CTD (with O2 sensor)\--Will start working next week when Roman returns
3.&nbsp; MOE to be opened right after this meeting
4.&nbsp; Gordon preparations. \--We are behind in preparing the sphere.&nbsp; MOE currently running a phase outside the ball.&nbsp; Chris will load new reagents today, and Monday we will marry MFB with core and move core to the sphere.

\--Will immediately initiate high-pressure testing.

5.&nbsp; Plans for next week's collaborators meetings* ESP team planning meeting next Thursday 10-1
* Thursday.&nbsp; UW.&nbsp; Agenda will have 1hr for MBARI, 1 hr for UW.&nbsp; maybe quick tour.
* Friday.&nbsp; ASU.&nbsp; Tour and then talks\\
h3. Announcements

* We have rec'd confirmation that the Moore Foundation grant was approved for development of new (smaller, faster) analytical module back ends.&nbsp;&nbsp;
* Announced Mechatronics meeting if publishing engineering papers is desired.]]></property>
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<property name="body"><![CDATA[Present:&nbsp;&nbsp; Jim, Bill U., John R., Chris P., Doug, Elif, Allison
Absent: Julie, Roman, Chris S., Vanessa

{color:#3300ff}1. Items:{color}\\
* Gordon and D-ESP&nbsp; preparation
** Temperature calibration finishes today.&nbsp; Tomorrw (Weds) will run phase.
** Join MFB and Core on Monday.&nbsp; Changing all core reagents Monday. &nbsp; Mount joined MFB/core into ball on Monday
* Uncanning triple deployment
** Mack/Bruce both had hand issues.&nbsp; Mack worse.
** Will uncan THURSDAY
** need new power to Moe and start investigating MOE Thursday
** pick up forensics on Mack and Bruce on Monday.
** John wants LISST off Bruce before we wash
* Allison leaves Dec 11.&nbsp; Will meet with Jim and Chris to discuss direction.
* Chris P. will have PCR paper draft on Thursday.
* Temperature testing (Elif)
** currently visual testing down to 2C
** She'll have more reagent when we swap out Gordon.&nbsp; Even more from Moe and Bruce; must wait until Roman gets back.

h4. Other items
\\

Doug going in Jim's place on tomorrow's recovery.

Shana and Adam from Spyglass may also go. ]]></property>
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h3. Tech Transfer

* Although only calibrated to room temperature, Neo is ready to make lysate.&nbsp; After a positive result, will run DA tests, then remove those reagents and finish cold and hot calibrations.&nbsp; Then give to science for exercise.
* Moe: waiting on boards, motors, and machined parts.&nbsp; Scott pushing to have boards finished by early July.
* Must determine where AIV valve will go when merging MFB on Moe core, and update solid model ({color:#ff0000}To Do: Addie/Cheri/Scott/Chris S){color}
* &nbsp;

h3. MFB

* Despite repeated failures of the MFB, Chris S. states, "we are homing in on it...
* cc Addie any emails from LLNL
* Must address changing of power supply of heater/MFB/extraction ({color:#ff0000}Action:&nbsp; Addie & Scott{color})
* Next week will move MFB to Bldg A lab and then run stink-water T/W/Th after Chris P returns from Microbiology mtg.

h3. Software

* Mack's hand has stuck twice during the current deployment (now on day 8) and Brent thinks it's getting worse.&nbsp;
* Must get more people on the beeper system, and he will train Cheri & Scott how to fix.
* Brent will stay on Kevin about GUI development, though next deployment is in Fall.

h3. DWSM

* CDR will be 10am Tuesday, June 10.&nbsp; Will invite same people that came to PDR.&nbsp; Jim will get room.

h3. Other Items

* Laid out and discussed plans for 2009.&nbsp; Plans concentrated in 4 areas:
** development of 4K system, culminating in cruise to Axial seamount in Q3.
** bench testing of MFB/PCR either here or in S. Cal as part of the EPA epidemiological study.
** pier deployments in S. Cal for water quality
** drifter study culminating in HI deployment, again in Q3]]></property>
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<property name="body"><![CDATA[Present: Scott, Doug, Addie, Kevin, Jim, Cheri, Brent, Wayne

Absent:&nbsp; Chris S (in China)

h3.

h3. Machine Builds

* &nbsp;Moe now has GG's harmonic drive part of the hand.&nbsp; Cheri noticed that GG's lower hand is sticky; could be slider, could be bad motor.
* Bruce leak.&nbsp; Found that o-rings in processing clamp were noticeably cracked; replaced and re-ran; Nilo said new photos look good.&nbsp; Discussion with Doug on a different material that would not crack with our reagents.
* Mack;&nbsp; flush puck may still be stuck as it hasn't been used.&nbsp; will check after lunch
* Cheri busy ordering parts for other two cores.
* One cart has a flat tire.

h3. MFB

* Jose currently busy, but will be available in 1 week to do wiring harnesses; he'll build 2, send rest out for manufacture.
* Parts ordered for serial connector to core; should be here Monday/Tuesday
* 2nd grill:&nbsp; Addie writing scripts for PCR and SPE
* Encoder/Dwarf;&nbsp; Addie had interesting problem where MFB froze, but after shutting several open windows, control was regained....&nbsp; Dwarf losing thje encoder count has not occurred again, but unclear why.&nbsp; Rebooting fixed.
* Chris P. has run plasmids on NEO MFB, and now negatives are coming up positive.&nbsp; She still needs to do a full-decon, and may require longer hot bleach times.
* Chris P. is setting up for a BAC superphase, to be run with debugging on.&nbsp; Much preparation, so the actual run may not begin until Monday.

h3. Software

* &nbsp;Xlinx issue; Brent and Scott working in bldg B to try and understand how encoder counts are being lost/dropped
* Jim (and possibly Roman) are starting a Ruby commenting project.&nbsp; Ultimate goal is to write a 'users manual' for the ESP.

h3. DWSM


h6. +Sphere+

* Wah Chang has been notified of potential repair and is looking into their policy.&nbsp; Regardless, we will ship the sphere back to them for dye testing to make sure there are no other surface voids that HIP could not eliminate, but we can't see.
* Tapemation should be finished with machining this week.&nbsp; Doug to check.
* Min-K delivery has moved from 6 weeks to 11 weeks (ordered 9-22-08); Scott has called and waiting to hear compny update.
* Pressure test facility information (from Mark Brown):
{color:blue}\*\* Hi Mark,{color}

{color:blue}Given the size of your housing it will fit in our 72" dia pressure{color}
{color:blue}vessel which is rated for 5,400 psi. It was rated for 5,500 psi but the{color}
{color:blue}Navy Hyperbaric System Certification people said we had to have put a{color}
{color:blue}relief valve on the vessel that is rated at the max working pressure{color}
{color:blue}(5,500 psi). To be on the safe side, we only go to 5,400 psi.{color}

{color:blue}The daily rate is still $1,800 until Jan. 1, 2009 then it will be{color}
{color:blue}$2,100.00. December is open except for the week of the 8th and from the{color}
{color:blue}25th till Jan. 5th.{color}

{color:blue}If you need more information then please give me a call or Fernando{color}
{color:blue}Ruiz. (805) 982-2054{color}

{color:blue}Thanks,{color}
{color:blue}Mark{color}

{color:blue}Mark Wells{color}
{color:blue}NFESC, Deep Ocean Simulation Facility{color}
{color:blue}1100 23rd Ave{color}
{color:blue}Port Hueneme, CA 93043{color}

{color:blue}v (805) 982-1531{color}
{color:blue}c (805) 766-8389{color}
{color:blue}f (805) 982-1938{color}

h6. +DWSM+

* &nbsp;Doug has sent up warning flare that our first DWSM deployment is rapidly approaching (Feb. 23), and we should start upper level programming of DWSM in parallel with the lower level testing that can currently occur.&nbsp; Brent/Wayne/Scott working on getting both upper and lower level testing up and running.
* Many parts to be ordered for elevator.
* Doug wants first deployment to be test of elevator with surrogate sphere (weights) to test deployment/recovery procedures.&nbsp; The next deployment we should have sphere pressure-tested and can add to the elevator.

h3. GUI Development

* &nbsp;Chris P. working with Kevin to better incorporate data processing within Alfresco

h3. Other Items:

* &nbsp;Thanks to Scott for an excellent job at cleaning the high-bay post-deployment and also the Bldg B clean-up.
{note:title=Remember}Please remember to use ESD straps in the bldg A lab, as most of its chairs and countertops have failed ESD testing.&nbsp; Dick Littlefield looking into seat-covers that are ESD compliant.
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# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## ESP Configuration In Lab
### Mission plan is created
### Pucks are loaded
### Reagents are loaded
### Mission script is loaded
## ESP Deployment
### Shore station is configured
#### Nothing from a GUI perspective
### FTP file store is configured
#### Once the FTP server is up and running, the user will log in to the ESP web site
#### If no mission has been created, the user creates a new mission for the ESP (can be empty)
#### The user configures the mission FTP server in the web application
##### Protocol (FTP/SFTP)
##### Server hostname
##### Port number
##### Base directory for deployment files
##### Username (or anonymous)
##### Password (or email)
##### Name and location of the log file (default is deduced from the type of mission e.g. real -> real.log)
#### The user saves the FTP configuration in web application
#### The user logs out
#### Server spins up a monitoring worker process that points to the FTP server configured for the mission
#### Process crawls FTP server site and examines each directory and file
#### If the directory/file is different that what is in the deployment directory in the ESP repository, sync file from FTP server to repository.
#### Update catalog entry for directory/file
#### If the log file was updated, spin up process to parse the log file.
### ESP mobilized on ship
#### Verify the ESP if functioning properly by checking files on the FTP station
##### Make sure ancillary instruments are logging
##### Check for any errors
##### Makes sure environment sensors are reporting that all systems are go (humidity, power, etc.)
### ESP deployed
#### Monitor ESP log files during deployment as was done in mobilization.
## ESP Operations
### ESP is sitting idle
### ESP processes sample
### ESP errors and halts
### Operator interacts with ESP
## ESP Data Analysis
### User enables image analysis
#### The proper GAL file is uploaded to the mission repository
#### The application sees the GAL file and does an automated analysis of the images.
## ESP Recovery
### Recover ESP with ship
### Demobilize the ESP off the ship
### Decommission the FTP server
### Decommission the shore station
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# Interface Documents
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
## [Real-Time ESP state update protocol framework]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Data Repository]
# [Developer Documentation]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Glossary]
# [Assumptions]
# [Outstanding Questions]
# [ESP Java GUI]
# Original [ESP GUI Users Guide]

Meeting Notes
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
# [01/11/2012 *GUI Update and Planning Meeting*|2011_01_12]

Presenations for GUI Development

# [6/6/2007 PDR Powerpoint slides|^PDR.ppt]
# [6/6/2007 PDR Work breakdown spreadsheet|^PDR.xls]
{panel}
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<property name="body"><![CDATA[Present:&nbsp; Chris P., Doug, Brent, Jim, Scott, Cheri, Julie, Sara, Sunni, Wayne

Absent: Chris S., Roman
\\

h2. &nbsp;Issues:

1.&nbsp; NONE\!

h2. Methane cruise

ISMS

1.&nbsp; Wayne and Sunni have wrestled the beast into submission these past 2 days, and are waiting on new o-rings to seal up the instrument.&nbsp; They will Can, Test, replace membrane, and be ready to go.&nbsp; Doug will take housing early next week for elevator build.

2.&nbsp; Slight issue with getting turbo pumps up to speed, but Sunni says this is normal--keep sending them 'go' commands and they eventually get going.

3.&nbsp; We will turn ISMS on once it reaches the bottom, and not turn it off until it a.)runs out of battery, or b.)mission ends.

DWM

1.&nbsp; Replaced IEP pump with the smaller one and now it (inexplicably) is working.

2.&nbsp; Plan is to exercise the sampling today, and sometime this weekend run a full day phase at temperature and pressure.&nbsp; Sunday will turn off the van and allow a slow warm-up.&nbsp; Will cut-out and SPE parts of the phase to spare the column of potential inhibitory effects of rust.&nbsp; Doug will then get it Monday to begin the elevator build.&nbsp; Scott and Jim to get more foam from Castroville this PM.

3.&nbsp; Logisitics:
Advance team will be Doug P., Brent, and Chris P., who will fly to LA on July 20, meet van, and fire off deck phase. They will spend evening in hotel arranged by Theresa C.
Rest of team arrives July 21; shove off July 22.

Scott is travel contact person week of June 21.&nbsp; DougP. contact person week of June 28.&nbsp; Jim takes back over week of July 5.


h2. M0 Flip

1. Lowering bubble-point pressure to 60PSI has worked and Moe has now made it through 4(\!) WCR's.&nbsp; Brent thought issue to look at was the raw counts of the pressure gauge while&nbsp; puck is in clamp and there was no pressure and while it was holding pressure.&nbsp; This would tell us if sensor is reaching it's limit due to wrong gains/offsets.&nbsp; Julie going to look at gathering that data.]]></property>
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<property name="body"><![CDATA[h2. ESP weekly meeting (Dec 20, 2007)

*Present:* Cheri, Scott, Chris P., Jim, Addie, Chris S.

*Tech Transfer*

&nbsp; &nbsp;Light seals changed?
{color:#3300ff}yes{color}

•&nbsp;&nbsp; &nbsp;Status of slow-running intake
{color:#3300ff}Need to check this out with GG.&nbsp; Science may not be needing it; Chris will Check. Scotts concerned that lower pressure sensor has changed its calibration by 50%.&nbsp; Would like to remove it to look for fouling.&nbsp; Chris mentioned 'blowing-up' a fragile bug because of larger pressure differential; sensor could be culprit.{color}

{color:#ff0000}ACTION:{color} is science finished with GG (Chris S)&nbsp;

{color:#ff0000}ACTION:{color} remove GG lower pressure sensor and examine (Scott)&nbsp;

•&nbsp;&nbsp; &nbsp;Status of manipulator hands.&nbsp; How many needed?&nbsp; How many made?&nbsp; Where are those installed?&nbsp; Waiting on any parts for hand?
{color:#3300ff}Still futzing with first redesigned hand.&nbsp; Very touchy assembly. Have 3 built but have found a problem with cam motor-mount.{color}

{color:#ff0000}ACTION:&nbsp;{color} meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)

•&nbsp;&nbsp; &nbsp;Status of motors and motor-mounts?
{color:#3300ff}Have all motors.&nbsp; Have all mounts.&nbsp; Mike is modifying encoder gears.{color}

•&nbsp;&nbsp; &nbsp;Any questions about published timeline?
{color:#3300ff}Will be using piezo-arrays for all these testings.&nbsp;{color}

{color:#ff0000}ACTION:{color}&nbsp; Need a Gantt chart of instrument usage (Jim)

•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?
{color:#3300ff}they sent a drawing of what they planned on doing (2 weeks ago?).&nbsp; Scott replied; do it.&nbsp; Haven't heard from them yet.{color}

{color:#ff0000}ACTION:{color} call and find out where they are (Scott)

•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?

{color:#ff0000}ACTION:{color} Must check with Jose.&nbsp; He's adding up inventory.&nbsp; Will need enough for 2 cores and 8 MFB and spares (at least 1 full core and enough spares for 8 MFB's\[3 dwarves, 2 R's\]).&nbsp; Tally up, look at production run, and scale up for best economy.&nbsp; Will place order early January. (Scott)

•&nbsp;&nbsp; &nbsp;Discussion of IP tech transfer w/ LLNL?
{color:#3300ff}Update:&nbsp; we have written agreement with LLNL that UH, WHOI, is aproved.&nbsp; Foreign use is unknown and Patrice is looking into it.&nbsp; Valve design TBD{color}

{color:#ff0000}ACTION:{color}&nbsp; Clarify IP on valve design (Chris)&nbsp;

*MFB*
•&nbsp;&nbsp; &nbsp;What will be MFB status as of 12-21-07?
{color:#3300ff}Solid phase extraction working well.&nbsp; Running through lysate coil on AIV.&nbsp; Slug still shows a gradient, first 100ul good, second 100ul (over column) has high concentration.&nbsp; Going to try just pushing 100ul through.&nbsp; Unable to find mixing chambers, so will only take 100, push to and fro a few times and it'll be mixed.&nbsp; Chris P thinks it may be TOO concentrated, bench rocovery is 12-25ug, and extrction is 25ug minimum.&nbsp; Still tweaking this.&nbsp; This will be January focus.&nbsp; Standardize the protocol for this.{color}

•&nbsp;&nbsp; &nbsp;When will all parts be in for 2nd MFB?
{color:#3300ff}All parts are in except MAXON motors.&nbsp;&nbsp; Cheri ordered 33 total, 27 for her and 6 for Addie (who has used 4, 2 are around MBARI) and needs to order 6 more.&nbsp; Cheri will use 24 w/ 1 spare apiece.&nbsp;{color}

{color:#ff0000}ACTION:{color}{color:#000000}&nbsp; place order with MAXON for MFB spares (Addie){color}

•&nbsp;&nbsp; &nbsp;What is left in extraction protocol?&nbsp; {color:#3300ff}Finalization of protocols will be early January.{color}

{color:#3300ff}{*}Chris Scholin hosting CMORE workshop Jan. 14-17 (35 people from OR, HI, WHOI) to define functional requirements for our and other partners CMORE work.*{color}{color:#3300ff}&nbsp; Suggests that we clean up MFB and put on cart, and do a demo run.&nbsp; Get rid of power board and zip tie things and tubing wraps, etc.{color}

{color:#3300ff}Dscussion about LLNL, when they will get a new block to us.&nbsp; If we get the driver block, we should have it out for display.{color}

{color:#3300ff}Discussion about PSV valve.&nbsp; Addie will add the PSV valve.&nbsp; Discussion about connections b/w core and MFB.{color}

{color:#ff0000}ACTION:{color} Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addie will figure out how to connect ports 3, 5, 6 with no bubbles. (Addie)

{color:#ff0000}ACTION:{color}&nbsp; Lubricating syringe.&nbsp; Must be 'upside-down' to prime with no air bubbles.&nbsp; But then could rotate 180 so it retains lubricant. Investigate remounting this right-side up after priming (Addie & Scott)

{color:#ff0000}ACTION:{color}&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (Scott will email)

*Software*
Brent gone until Jan 2nd.

*Sphere and 4K DWSMS*
•&nbsp;&nbsp; &nbsp;Sphere ordered by Jon Erikson on Dec 13, 2007.

*Funny Money Expenditures*
•&nbsp;&nbsp; &nbsp;Currently getting quote on 3 cans/endcaps; do we need for current year?

{color:#3300ff}We have two complete surface moorings (although one can is a 'spare').&nbsp; Will turn off mooring hardware PO from 2006.{color}
•&nbsp;&nbsp; &nbsp;Pucks?

{color:#3300ff}Mike will have a quote tomorrow.{color}
{color:#3300ff}big expenses should go through Chris S for spreading charges among accounts.{color}

*Issues from Doug:*

•&nbsp;&nbsp; &nbsp;Serial numbering of pucks.

{color:#ff0000}ACTION:{color} Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott)

•&nbsp;&nbsp; &nbsp;Image reflections on puck.&nbsp; Still and issue?
{color:#3300ff}no{color}
•&nbsp;&nbsp; &nbsp;Concern on cleanliness of SSfittings off deep chamber
{color:#3300ff}We are only using electrical connctors, not fluid connectors. May have to order fluid fittings for 'box test'.{color}

{color:#ff0000}ACTION:{color} look into need for new fluid fittings and order if necessary (Cheri)

•&nbsp;&nbsp; &nbsp;Pressure pots; rust source?
{color:#3300ff}Will clean and should be okay.{color}

{color:#ff0000}ACTION:{color} Cheri to get pressure pot sizes to figure box structure. (Cheri)

{color:#ff0000}ACTION:&nbsp;{color} Pressure posts. We want this inventory: 2 fives, 2 tens, 2 threes.&nbsp; Must order enough to reach this inventory (Chris P)

•&nbsp;&nbsp; &nbsp;Battery/power issues for spring deployments
{color:#3300ff}stick with alkaline.&nbsp; Do we need more boxes?&nbsp; Need 4 boxes initially.&nbsp; Not working on low power issues.&nbsp; Must order minimum of 1 box of batteries in early 2008.{color}

*4K stuff:*
1. I have lower, more reasonable quotes for the sample chambers, but
they're trepanning solid stock so it's still pricey. It is something
that we could do or have El Camino do instead. I'll need to touch base
with Mike to see if it's worth while. Maybe a competitive quote from El
Cam.
2. We don't have a lot of time (20 weeks lead time on these) but I'm
looking into a steel housing to proof the system before. End caps and
penetrators would still be TI, but $40k would buy a lot.
3. I've made some small (but measureable with an interferometer)
progress on the 1k article.

*Timeline (This schedule is its own page in Confluence):*
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.

{color:#3300ff}Cold testing of Bruce is really just 'hand' cold-testing.&nbsp; Valving and tubing tests commence with Ma{color}ck.

*Items Pending:*

battery box
stedim bags for aqualung&nbsp;
Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp;
Three new surface cans for 2008&nbsp;]]></property>
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<property name="body"><![CDATA[Subject: Machining 4k sphere
Date: Wed, 5 Dec 2007 08:25:41 \-0800
Thread-Topic: Machining 4k sphere
Thread-Index: Acg3W3pDdPq8Hs8jRtKanjDmUGXOrA==
From: "Brown, Mark" <mob@mbari.org>
To: "Birch, James" <jbirch@mbari.org>,
&nbsp;&nbsp;&nbsp; "Scholin, Chris" <scholin@mbari.org>

Jim & Chris\-
Just to keep you up to date\-
For machining the large 4k sphere's we have one quote from our local vendor (Tapemation) that came in approx. $40,000. *We had another vendor in Oregon just get back to us with a "no quote" and they said this was outside of their comfort zone.*
&nbsp;
I have a call into our casting vendor Wah Chang asking about who they might have dealt with for a large casting such as this and I will let you know what I find out.
\-Mark
Mark Brown
Support Engineering&nbsp;Group Leader
MBARI: <[http://www.mbari.org]>www.mbari.org
ph: 831 775 1939
fx: 831 775 1615]]></property>
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<property name="body"><![CDATA[h2. Engineering weekly meeting (Dec 6, 2007)

*Birch Absent.&nbsp; Notes by Jensen...*
# Software situation
*2 bugs*

## Continuation
## Dead Parents

Enough runs yet?# NEO completes 5 runs continuously, should we run 5 more?&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;
Concern is we may run low on reagents.&nbsp; No, hand over to science now that Brent has handle on where two bugs are.

We will stay with Ruby v. 1.6 and leave Neo as is.

*&nbsp;NEO*

Cheri will change light-seal next week&nbsp;&nbsp;
Software will remain unchanged
intake is running slow--must check
science to find problem with arrays&nbsp;

*Manipulator Redesign*

Redesigned fingers are working well
Forearm
&nbsp;&nbsp;&nbsp; motor pulley good
&nbsp;&nbsp;&nbsp; front needs to be finished
Cheri waiting on machining of several arm parts and arrival of bearings.&nbsp; Should be in tomorrow.

*&nbsp;MFB*

Good results from first SPE run; good DNA yield

Concerns with SPE heater

\*&nbsp;&nbsp;&nbsp; fluidic bubble heating
\*&nbsp;&nbsp;&nbsp; loading and eluting at 2 different temperatures
\*&nbsp;&nbsp;&nbsp; will work toward thermal profiling
\*&nbsp;&nbsp;&nbsp; Add relay heater with solenoid

*LLNL*\--they rec'd the heater Thursday, Nov 29, 2007. &nbsp; &nbsp; Tony's email of Monday, Dec 3, 2007:
{quote}
Jim,  We got the block last Thursday. So far we have looked it over to see if anything was disconnected or obviously wrong with it.  It looked fine. We have tested the LED's and DIODE's.  They seem to be responding as expected, giving increasing response to increasing integration times and increases with the LED on vs off. At this point, I'm going to go ahead and tune it up and try a PCR reaction in it with the same reagents that I sent to you.  Should be able to get to you with some results by the end of the day Wednesday.  Tony
{quote}
Discussion ensued about a Waste container.&nbsp; Engineering will look into a hard volume waste bottle w/ filter and possibly hydrophilic gel similar to Cepheid or that used in scrubbers (chris P).

All parts for 2nd MFB have been ordered.&nbsp; Will arrive next year (Jan. 2008)&nbsp;

Possible concern:&nbsp; Burkert website says solenoid valves may be discontinued.&nbsp; Addie will check on.VICI valves&nbsp;&nbsp;&nbsp; order more for 2 spares
*Puck Heater*

&nbsp;&nbsp;&nbsp; Scott has developed a good model for temperature control via a modified puck sensor finger
&nbsp;&nbsp;&nbsp; We need to run a full mock mission (1 month) with acrylic can within our environmental chamber.

*Science Stuff*
&nbsp;&nbsp;&nbsp; Chris almost finished with NOPP proposal.&nbsp; Scott & Brent to look over SOW.&nbsp; Due Friday.

&nbsp;*FUTURE*
&nbsp;&nbsp;&nbsp; must work out deployment schedule for network deployment
&nbsp;&nbsp;&nbsp; which instruments will be going and with what configuration?
&nbsp;&nbsp;&nbsp; fitting in testing for these instruments and rework time.&nbsp;]]></property>
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<property name="body"><![CDATA[h4. ESP Science Users meeting

Issues:

h5. Chris P.

# PCR paper in Scholin tempbox.
# Will start samples collected at diffuse vent field at JdF in 2004 later this week.

h5.


h5. Elif

# Currently QC'ing new capture probes.&nbsp; Will help with cold testing Bruce once Bruce is reassembled and cold calibrated.

h5. &nbsp;Roman

# &nbsp; Bruce being reassembled and will perform the room temp tests today.&nbsp; If passes, then goes in cold today, and hopefully have GOM qualifications this week.&nbsp; Will try and have MOE reassembled by next week.&nbsp;

h4. &nbsp;OTHER ISSUES:

&nbsp;Will send ASU template next week when Julie filters seawater collected Monday (2-28-2011)


WHOI needs Notice-to-Mariners filled out for ESP-Bruce.&nbsp; Mike Kelly needs following information (from 2-22 email to Birch):{color:#3300ff}I coordinate the local (California) NTM's.&nbsp; Could WHOI provide the contact email for the Gulf of Maine deployment?{color}
{color:#3300ff}&nbsp;{color}
{color:#3300ff}Some detailed information is required:{color}
{color:#3300ff}&nbsp;{color}
{color:#3300ff}Depth and Lat/Long (as close as possible){color}
{color:#3300ff}Size and color of the surface buoy{color}
{color:#3300ff}Nav light flash interval and color&nbsp; (e.g. Yellow, 1 sec ON, 4 sec OFF){color}
{color:#3300ff}Deployment and recovery dates (anticipated){color}
{color:#3300ff}&nbsp;{color}
{color:#3300ff}Also, a brief description of the project - usually 2-3 sentences.{color}
Waiting on info from Bruce Keafer

&nbsp;Requested HV pucks from McLane.&nbsp; Ivory said they are being worked on as we speak.]]></property>
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<property name="body"><![CDATA[# [2008 Q1-Q2 Schedule (rev 1)]
# [2008 Q1-Q2 Schedule (rev 2)]
# [2008 Q1-Q2 Schedule (rev 3)]
# [2008 Q1-Q2 Schedule (rev 4)]
# [2008 Q1-Q2 Schedule (rev 5)]
# [2008 Q1-Q2 Schedule (rev 6)]


# [Machinist build schedule (Feb 2008)]]]></property>
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<property name="body"><![CDATA[h2. &nbsp;Outline of instrument plan for Jan-Jun, 2008

Mack has been cold tested with new hand and new valves and Roman Flush run to check tubing.

Temp calibration Jan 29-31.

Feb 5,6,7 Science will prep reagents, generate mission script, run sub-protocol tests&nbsp;
# One month cold test of Mack w/ his new valves/hand starting Feb 11.
## OBJECTIVE:&nbsp; get through a full carousel of pucks
## test should last most of 4 weeks (although 3 weeks would be acceptable)
# March 3 is earliest we pull and deem a success.&nbsp; Once pulled, we replace with Bruce in chamber.&nbsp;
# Prep for Spring deployments (Mar 26-->Mar 27)
# {color:#ff0000}{*}Deploy{*}{color} MACK (April 1-Shana Rae)
#- Cold test Bruce (Mar 17 - Mar 28) and Neo (Mar 31 - Apr 11)
# &nbsp;{color:#0000ff}{*}Recover{*}{color} MACK, {color:#ff0000}{*}Deploy{*}{color} BRUCE (May 1)
# {color:#0000ff}{*}Recover{*}{color} BRUCE (May 27), {color:#ff0000}{*}Deploy{*}{color} *both* MACK and NEO (May 28)
# End mission Jun 30.
\\
\\
\\
\\
\\
\\

(Revised 29 Jan 2008)&nbsp;]]></property>
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<property name="body"><![CDATA[h2. Engineering weekly meeting (Nov 29, 2007)

Present: Birch, Harris, Scholin, Everlove, Pargett, Roman&nbsp;

*Tech Transfer*
•&nbsp;&nbsp; &nbsp;Status of Bruce and Mack (and Moe)
•&nbsp;&nbsp; &nbsp;New hand construction update
•&nbsp;&nbsp; &nbsp;Status of new motors/ new motor brackets
•&nbsp;&nbsp; &nbsp;Cepheid coming Friday?

{color:#0033ff}Bruce and Mack are 97% assembled.&nbsp; Both lack hand, which only has slider issue to resolve, and all can be modified.&nbsp; Have ordered more blue nipples and tubing; should arrive end of this week (tomorrow?).&nbsp; 27 Maxon motors shipped yesterday.&nbsp; El Camino has not started machining new motor brackets because they lost our PO and the job fell out of que.&nbsp; Mike Parker will push to make them meet their original Dec. delivery date.{color}

{color:#0033ff}Cheri to order enough syringes to completely outfit Bruce, Mack, Moe, plus have a spare set.&nbsp; These are COTS.&nbsp; Scott still working to get custom, cold-rated syringes built.&nbsp; Break charge in thirds among 800560, 703506, 900612.{color}

{color:#0033ff}New motors to be placed on Bruce, Mack, and Moe; no changes to NEO and GG.&nbsp; Dwarf boards--we have enough for Moe, but then no extras.&nbsp; Must meet with Scott about new order.{color}

{color:#0033ff}Cepheid IS arriving for visit tomorrow, 10am.&nbsp;{color}

{color:#0033ff}Chris S. says NOPP proposal generating much interest in PCR module.&nbsp; Sandia, Stoneybrook, U Maine all have detection technologies they would like to use with our fluidics layout.&nbsp;&nbsp; We must clarify IP issues with LLNL about transfer of fluidics (not PCR) technology to other parties.&nbsp; Also will impact how many dwarves to order.&nbsp; Have requested letters of support from us for their NOPP proposals.&nbsp;&nbsp; WHOI is taking our specifications for syringe assembly for their in-situ flow cytometer.&nbsp; A similar tech transfer agreement can be made to these other institutions once IP with LLNL worked out.&nbsp; Don Kennedy here next Weds; Chris giving a tour with NEO in test-tank area.{color}

*MFB*

•&nbsp;&nbsp; &nbsp;Status of adding AIV and new ASV
•&nbsp;&nbsp; &nbsp;Mounting of solid-phase extraction hardware
•&nbsp;&nbsp; &nbsp;Status of new script development
•&nbsp;&nbsp; &nbsp;Heater block sent to LLNL
•&nbsp;&nbsp; &nbsp;Prediction for 12-21-07?

{color:#0033ff}ASV now mounted and Addie's pushing water through.&nbsp; AIV still waiting on mounting brackets from El Camino. Script written to control valves without AIV.&nbsp; SPE mounted and moving water.&nbsp; Heater is easy to control.&nbsp; Chris has rec'd 12 more small columns and 12 holders.&nbsp; Addie will get one to Mike Parker to build another heater.&nbsp; PCR heater sent back to LLNL on Tuesday (11-27) and FedEx has it arriving 11-28 at 9:01am.&nbsp; Still to hear from Tony if it arrived.&nbsp; Hope is to have SPE working by 12-21.&nbsp; Fluidics will be ready by tomorrow.&nbsp; Then it is biochemistry testing.{color}

{color:#0033ff}Must still develop decon script for the SPE column/tubing.&nbsp;{color}

*Software*
•&nbsp;&nbsp; &nbsp;Tracing the Ruby garbage error...
•&nbsp;&nbsp; &nbsp;Plan for low power processor visit
•&nbsp;&nbsp; &nbsp;Progress of Bob Herlien on MFB drivers?
•&nbsp;&nbsp; &nbsp;Progress of Rich Schramm on GUI?
•&nbsp;&nbsp; &nbsp;JIRA?

{color:#0033ff}Brent able to reproduce the error, but cannot identify where it is occurring. &nbsp; Took debugging scaffolding and ported to run on the core processor and now is able to reproduce the error in a repeatable spot.&nbsp; He knows the structure and block that's getting messed up; perhaps modifying C-debugger to run code slower...{color}

{color:#0033ff}Work this week/end at pushing pucks through and reproducing the error.&nbsp; If no progress by Monday, then work on creating a 'test case' that would allow sending to other developers, who would run this code without the need for hardware.{color}

{color:#0033ff}Low power CPU visit postponed, but decision to change to lower powered CPU will wait, as the market is already moving in that direction.&nbsp; With this 'job' off the table, Jim will visit with Wayne R. about his timeline in 2008.{color}

{color:#0033ff}Bob Herlien has PCR driver multi-threading finished and awaits hardware to test in on.{color}

{color:#0033ff}Rich Schramm pulled off ESP GUI development for 2 weeks for MARS work; we will get him in January.&nbsp; Plan is to use GUI during spring '08 deployment, which means we need it to fiddle with by \~March, '08.&nbsp;{color}

*Sphere and 4K DWSM*
•&nbsp;&nbsp; &nbsp;Ordering sphere
•&nbsp;&nbsp; &nbsp;Still awaiting machining quote from Hanard Machining, Oregon.
•&nbsp;&nbsp; &nbsp;DWSM---need for mechanical design (Doug's return?){color:#0033ff}Jim will start PO process for sphere today.&nbsp; Jon Erikson will be contact (backed up by Mark Brown).&nbsp; Hanard has (as of yesterday) not completed their machining quote.&nbsp; Doug will begin DWSM work when he returns in January.{color}]]></property>
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<property name="body"><![CDATA[Here is the Logo: !ESP logo color.png|thumbnail!

h2. Below are some high-resolutions formats you may like:

[B&W .PDF|^ESP logo bw.PDF|b&w PDF]

[B&W .TIFF|^ESP logo bw.tif|b&w tiff]

[Color .PDF|^ESP logo color.pdf|color PDF]

[Color .TIFF|^ESP logo color.tif|color TIFF]

There are other formats attached to this page (go to the attachment tab above and download directly)]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Scott, Brent, Doug, Jim, Gene

Absent:&nbsp; Chris S., Cheri, Addie, Wayne

h3. Machine Builds


h3. MFB


h3. Drifter

* Pre-Flyer cruise dive days on the Zephyr have been pushed back to May 26 and May 28
* Gene will be in Test Tank Monday/Tuesday
* Ordering radar reflector.&nbsp; Have blinky light.&nbsp; PPP is running via wire.&nbsp; Scott will set-up Freewave's
* If time, will pull Iridium off an existing surface mooring and mount on Drifter.

h3. Software

* Brent's been working on HP pump.&nbsp; It seems to run either full on or off.&nbsp; Difficult to run it at other than 2000rpm.&nbsp; He has a was to work servo control with this constraint.
* Next is to characterize the differential pressure sensors then
* run sample fluid through the core loop
* Noticed that TSV seems to get off by 7-9 counts when you power cycle. Scott will watch while they try and re-create.
* Discussion about making the laptop on the boat a 'slave' to the shorestation, so missions can be started right on the boat (boat laptop\--> shore station-\->ESP buoy) instead of having to rely on someone on the shore.

h3. Deep ESP


h6.

* Will talk to Science about needs for a metal wand to withstand high temperatures at Axial.&nbsp; Otherwise, with current design, the end of the 'wand' is actually a solenoid valve.
* Doug showed valve design to Brent and explained function.
* Must get Science buy-in about wand idea, but in the meantime we will push forward with this design.

h3. GUI


h3. Deployment Issues

* Two potential sites to visit in June:
* \#1.&nbsp; 2900m \[36.61N, 122.44W\].&nbsp; Flat, open, clear water.&nbsp; Nearby clam-field.
* \#2.&nbsp; 1800m \[36.71N, 122.1W\].&nbsp; Flat, poorer visibility.&nbsp; very old whale-fall.
* Much discussion of which site.&nbsp; Consensus was that August cruise is most critical (depths of 1400-1600m), thus site #2 would provide adequate testing for August without undue risk.&nbsp;&nbsp;
* A very rough deployment schedule was discussed.&nbsp; Leave MBARI @ 11am on Friday, June 5, return Tuesday, June 9.&nbsp; Chris and I will meet with ship crew 10am (Tank View) Tuesday to discuss.
* 4K ISUS mtg Tuesday @ 11--Tank View.&nbsp; Will meet with Luke, John R., and science.

h3. Other Items:]]></property>
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<property name="body"><![CDATA[h2. *ESP Engineering weekly mtg (11-15-2007)*

Present: Jensen, Scholin, Everlove, Birch, Harris

*Tech Transfer*
•&nbsp;&nbsp;&nbsp; Still on track to have 2 instruments wired & plumbed by Thanksgiving?
2 units almost completely wired (boards/valves/motors).&nbsp; End of day both powered.&nbsp; Plumbing parts in yesterday and will continue this afternoon.&nbsp; Do 2 units first then retrofit Neo.

•&nbsp;&nbsp;&nbsp; Hand/puck sticking issue?&nbsp; (still working on)&nbsp; New hand design?(getting close, tackled pivot-point and the cam,&nbsp; but still figuring how to support forearm pulley so belt can be fully loaded)

•&nbsp;&nbsp;&nbsp; Science getting to use yet?
Using GG. Don't need Neo

•&nbsp;&nbsp;&nbsp; Time for delivery of new motors/brackets?
Still waiting on brackets (Mike supposed ot have sent PO to El Camino yesterday) and motors (due end Nov).

•&nbsp;&nbsp;&nbsp; Other issues

If some grants come in, we will have many instruments needed around the country.&nbsp; Chris is pushing for building all three (don't leave one as parts).&nbsp; In the near future we will need another production run and should keep in mind parts for the future.

*Software*
•&nbsp;&nbsp;&nbsp; Progress in Tracing of log comments?
•&nbsp;&nbsp;&nbsp; Bob Herlien progress on MFB drivers?
•&nbsp;&nbsp;&nbsp; Rich Schramm progress on GUI?
•&nbsp;&nbsp;&nbsp; JIRA implementation
Discussion of these items tabled since Brent is gone.

*MFB*
•&nbsp;&nbsp;&nbsp; Results from Tues/Weds and subsequent plan going forward
•&nbsp;&nbsp;&nbsp; Solid-Phase-Extraction status
•&nbsp;&nbsp;&nbsp; CAV (AIV) valve arrival?
•&nbsp;&nbsp;&nbsp; Overall parts inventory; do we have everything we need?

Building slug on bench then pulling through the ARV and running in the MFB heater and collecting it after and looking at peak fluorescence and run on gel.&nbsp; WE HAVE AMPLIFICATION.&nbsp; Solutions seems to be due to better cleanliness and care in handling reagents.&nbsp; Optics within the LLNL heater block do not appear to be working properly.&nbsp; Today will actually _build_ the slug from the ARV and then repeat yesterday's successful procedure.&nbsp; If successful, will add ATV and repeat.&nbsp; Chris P. has ordered more fluorescent dye.&nbsp; When it arrives we will do a final test of the optics ourselves before we (most likely) must send the block back to LLNL.

*4K issues*
•&nbsp;&nbsp;&nbsp; Quote for casting the 4K sphere is here: [Wah Chang|^Wah Chang quote MBARI 60200 11-14 C5.pdf] and the quote for machining it is here: [Tapemation|^Tapemation quote MBARI 4K Hemi.doc]
•&nbsp;&nbsp;&nbsp; BOM for sphere, fittings, elevator, all accessories still being formulated.&nbsp; Plan to meet with Chris S., Scott, Jim next Tuesday to discuss BOM of 4k and DWSM

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<property name="body"><![CDATA[*ESP Engineering weekly mtg (11-08-2007)*

Present: Brent Roman, Addie Harris, Scott Jensen, Cheri Everlove, Jim Birch

&nbsp;Tech Transfer: Build of 2 new instruments moving along smoothly.&nbsp; New motor brackets being sent to El Camino for machining.&nbsp; That charge (~$3500) must be subdivided b/w various accounts.&nbsp; Wait to talk to Scholin about this.&nbsp; By Thanksgiving, both machines should be wired and plumbed.

Much discussion about puck sticking to O-ring, and possible fixes/re-designs.&nbsp; Scott looking into.

&nbsp;Software:&nbsp; Ported our code from v1.6.8 up to 1.8.6 and (unfortunately) found exactly the same errors at the same spot.&nbsp; Cannot be made to fail on the simulator, but fails on the actual instrument.&nbsp; Brent attacking this by tracing log comments.&nbsp; Brent attended Ruby Conference in Charlotte, NC and is interested in J-Ruby for our shore station. Will look into.

&nbsp;MFB:&nbsp; still not working but Chris and Addie have run a large number of experiments to try and isolate where our reagent mix is being 'killed'.&nbsp; Conclusion so far is that something within the fluidics block is inhibiting the reaction, since building slugs from the block show diminishing PCR activity the longer we wait to run on the 7700.&nbsp; Trying to build slugs only going through ARV, and other permutations to see where the contamination is entering.

&nbsp;Vacations discussed.&nbsp; Brent will be away for most of Dec.&nbsp; All others have short holiday vacations planned.

Discussion about starting to keep notes on Confluences, this record being the first.&nbsp; Question came up about how easy it would be to search Confluence records.&nbsp;
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<property name="body"><![CDATA[Present:&nbsp; Scott, Brent, Doug, Chris S, Jim, Gene, Kevin

Absent:&nbsp; Cheri, Addie, Wayne

h3. Machine Builds

* Harmonic drives in and Cheri working on switching them out
* McLane making progress on MFB's after I2C issue last week.

h3. MFB

* \#1 is on NEO.&nbsp; #3 is on Moe.&nbsp; Just Received #4.&nbsp; All are running firmware version 4.03.&nbsp; Also rec'd our fourth module (labeled #5).
* Tony Makarewicz leaving LLNL tomorrow, May 8.

h3. Drifter

* May 13 dive day moved to October; First drifter dive is Monday, May 18. it will consist of Chris S., Gene, Scott, Jim.
* will use the E/M cable, but with a sealed end and a RR rail piece as the weight.
* Code is still in rudimentary stage.&nbsp; Gene would like someone to ask Linux/ C+\+ questions of if he needs.&nbsp; Kevin/Danelle/Brian K were volunteered.
* Hope to get in test tank by end of next week.
* Chris S. will fill out pre-cruise
* ppp connection has not been worked on for a week.&nbsp; Brent will provide Pete with cheat sheet and freewave manual to help him get started on the configuration.

h3. Software

* Gordon will NOT get modified ethernet driver.&nbsp; Deployments will not be long enough to warrant the power savings by changing the hub in the sphere, and Wayne is not here to help with the driver change.
* Code currently resides on Neo branch, Main branch, and GUI branch.&nbsp; Much disucssion on when to merge;&nbsp; on Gordon in lab tests we'll use GUI branch.&nbsp; {color:#ff0000}After June cruise we will merge GUI line with main line and run checkout on Gordon then{color}.
* Wireless comms.&nbsp; Decision is to use Freewave's to communicate wirelessly with the sphere.&nbsp; This requires a MINK connector/fitting; Scott will scrounge up/buy.

h3. Deep ESP


h6.

* Wand/valve tree.&nbsp; Doug can only get SS valves.&nbsp; He using some that Cheri has.&nbsp; They need minor modifications to be oil-compensated.
* Cables for valve tree have been ordered; should be here in 2 weeks
* 50' of cable for wand delivery
* Some discussion of tubing needed for wand, but a McMaster item so little lead-time.
* Wand stand still to be designed.&nbsp; Most likely will be something like a microphone stand.
* Doug has plans for a sectional bumper design for Oregon cruise.
* DWSM restarted and all switches worked.&nbsp; Doug and Brent to meet after to find out what might have gone wrong.

h3. GUI


h3. Deployment Issues.


h3. Other Items:

Jim in late Monday; picking up TWIC card.]]></property>
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<property name="body"><![CDATA[h2. Quotes

* Sphere casting [(Wah Chang)|^Wah Chang quote MBARI 60200 11-14 C5.pdf] \[1st piece arrived May 7, 2008\]
* Machining
** [Tapemation|^Tapemation quote MBARI 4K Hemi.doc]
** Hanard Machine (sent for quote 11-15-07 \--> [negative response])
** Sphere pictures are located in [http://mww.mbari.org/ProjectLibrary/ESP/DWSM/4K DWSM/4k Sphere Pictures]]]></property>
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<property name="body"><![CDATA[{warning}This page is deprecated and this technique is no longer used. We're retaining this page for archival purposes{warning}

h2. Extracting _Spots_ from ESP Images

h1. The BIG Picture
The first step is to read the raw tiff image:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-spots.png!

h1. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h2. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h2. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn

// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutoContrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(acImage)).filter(_.eccentricity()._1 < 3)
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-ac-spots.png!

h2. Third Pass: Dynamic Contrast (Fuzzy-Sets)
{code}
import org.mbari.esp.ia.imglib.FuzzyContrastFn
val fuzzyContrastFn = To16BitGrayFn andThen FuzzyContrastFn
val fcImage = fuzzyContrastFn(rawImage)
val fcRegions = SpotRegionsFn(rawImage, rawFloodFill(fcImage)).filter(_.eccentricity()._1 < 3)
val fcPoints = fcRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(fcImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = fcPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-fc-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-fc-spots.png!]]></property>
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<property name="body"><![CDATA[h3. Administrative

(if asked to 'authenticate' in order to download anything, use 'shore/username' & then your MBARI password)
# [The MFB User's Manual]
# [MFB command help sheet|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1_7%2010_03_2008.doc]
# MFB chargers are Xenotronix HPX-30, and the batteries used are PowerSonic PS-12120 F2.

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/Fluidics_worksheet_04Dec08.pdf]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB BOM (2-28-2012)|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/BOM-REV%202012_02_28.xls]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes (no longer maintained--Sep 2012)

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [3G Cartridge-puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments](MB)
# [2009 Deployments](MB, MARS, SC Wharf)
# [2010 Deployments] (MB, SoCAL, Methane Mound, Drifter, MARS, SC Pier)
# [2011 Deployments](MB, GoM, Axial, Drifter-HI, SC Pier)
# [2012 Deployments] (MB, New Zealand, SoCAL, Friday Harbor, GoM, Drifter)
# [2013 Deployments] (MB, SoCAL, MARS, Puget Sound)
# [2014 Deployments] (MB, San Diego, Catalina, SoCAL, 3G)
# [2015 Deployments] (MB, SCRIPPS, 3G)
# [2016 Deployments] (3G in MB twice, SCRIPPS, Moran)
# [2017 Deployments] (3G, SCRIPPS...)
# [2018 Deployments] (3G, MB)
# [2019 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process.

h3. Requirements
|| Number || Requirement || Goal ||
| | User can define missions by specifying phases | Planning |
| | User can specify and adjust phase start times | Planning |
| | User can also specify a time to wait between events instead of a specific start time | Planning |
| | User can set mission start and end times that are not associated with a phase/protocol | Planning |
| | User can specify comments associated with missions that are printed at the top of the mission script | Planning |
| | After planning, application should generate mission script, puck loads, and reagent volumes | Planning |
| | User can add comments to a phase that will be generated in the script | Planning |
| | Users can add/delete/edit protocol runs and phases | Planning |
| | Users can load missions from existing ruby scripts | Planning |
| | Users can specify thresholding events in plans ([example|Mission Planning Script with Thresholding]) | Planning |
| | Users can copy existing phase and protocol to crate duplicate | Planning |
| | Users can add/delete/edit consumables | Planning |
| | Users can schedule Kills (end purges) or disable kills | Planning |
| | Users can define generic events and what script will actually be added to the master script (if needed) | Planning |
| | Mission plan generation will include a puck loading list | Planning |
| | User can associate external files with events (excel spreadsheet, documents, etc.) | Planning, Data Management |
| | Tide and phase information will be available | Planning, Data Management |
| | Application will list sample volumes with protocol run | Planning, Data Management |
| | User can add non-phase/protocol events (user defined) to the calendar anywhere | Data Management |
| | User can view images associated with phases | Data Management |
| | User can browse the .GAL file along with image and filter paper information | Data Management |
| | User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density | Data Management |
| | User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery | Data Management |
| | When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown | Data Management |
| | Application should allow for details of flushes to be seen/accounted for | Data Management |
| | The application should archive (and make available) the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts | Data Management |
| | Users should be able to download instrument logs and images and the GUI will parse out the following events:
* Track deployments of contextual sensors (sub-deployments of ESP)
* Collection of contextual sensor data (with capability to view/work with data) 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time | Data Management, State Visualization |
| | Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power | State Visualization |
| | Users can visualize the current state of the instrument | State Visualization |
| | Users can scroll back in time and visualize instrument state at the various points in time | State Visualization |
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<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = io.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}

!pcr11jun2520h2000ml40s.png!

h2. Extracting Bright Spots

The fiducials are typically the brightest areas on the image, especially in contrast to pixels immediately adjacent to the fiducial spots. We take advantage of this quality and isolate the fiducials by calculating the standard deviation of a 3x3 kernel across the entire image. The reason is clearly evident when looking at a surface plot of the raw image vs. the standard deviation. On the raw image, the fiducials may not be distinct from noisy backgrounds. However, when when using the standard deviation the fiducials sharply contrast with the rest of the image. In the images below, the 3 brightest peaks are the fiducial spots on the image.

!rawimage.png|width=900!
!stdimage.png|width=900!

We can extract the bright regions with the following code:
{code}
import org.mbari.esp.ia.imglib.BrightSpotExtractorFn
val regions = BrightSpotExtractorFn(rawImage)
{code}

{info:title:BrightSpotExtractorFn}
The internals of this function use a very standard pattern for spot extraction. The steps boil down to:
# Convert the image to 8-bit Gray so that we can calculate the histogram very quickly.
# Threshold the image using _maximum entropy_. _Renyi's entropy_ also works well but takes longer to calculate.
# Convert the binary threhold image to 16-bit *before* flood filling. Sometimes there is more than 256 regions, which can not be represented in an 8-bit image.
# Remove the area outside of a central circle. In general, we use a circle radius of 75% of the minimum radius of an image.
# Flood fill the image. Regions with less than 5 pixels are considered to be noise and are ignored.

Here's the function in it's entirety:
{code}
package org.mbari.esp.ia.imglib

import ij.process.ImageProcessor
import org.mbari.esp.ia.awt.ShortRegion

object BrightSpotExtractorFn extends (ImageProcessor => Iterable[ShortRegion]) {

    def apply(from: ImageProcessor): Iterable[ShortRegion] = {
        // Calculate local standard deviation for every 3x3 block of pixels
        val to = StdFn(from)

        val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
        val floodFill = {
            val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
            val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
            To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
        }
        val fill = threshold andThen floodFill

        SpotRegionsFn(from, fill(to))

    }
}

{code}
{info}

Then draw the image as follows:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val points = regions.map(_.centroid)
val circles = points.map(p => new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))

val colorImage = ToRGBFn(image).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
io.write(colorImage, new File("pcr11jun2520h2000ml40s-with-extracted-fiducials.png"))
g2.dispose()
{code}

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<property name="body"><![CDATA[h2. Meeting minutes stored in the projectlibrary:&nbsp;

# [Meeting Notes from June 7, 2007|http://mww.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc]
\\

h2. Meeting minutes stored within Confluence:

# [08nov2007]
# [15Nov2007]
# [29Nov2007]
# [06Dec2007]
# [20Dec2007]]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris P, Elif, John R., Roman, Allison, Bill, Chris, Jim

Absent: Julie R.

h2. &nbsp;Items Discussed:


h4.


h4. +1.&nbsp; Cold testing+

* Viscometer to arrive late this week
* Testing Idea:

# Place instrument at 4C and see if it works
# Let it warm up and start series at room temp.&nbsp; Use live culture in pressure pot to test system end-to-end.&nbsp; Do again with treatment 1 and trtmnt 2
# Drop temperature and repeat.

Test Matrix:
|| Temperature || wash/block alcohol %by v/v \\ || ||
| room | 5% | 10% | 15% \\ |
| 10 | 5% | 10% | 15% |
| 4 | 5% | 10% | 15% |
* We should plumb all three (5, 10, 15%) at once and change mission to pull from each for each run
* Before each run, pull out samples to run on bench for comparison.&nbsp; These will only be HAB arrays, (no DA).
* Initially think this will be on MACK.&nbsp;

h4. +2.&nbsp; Upgrade of NEO+

&nbsp;There is strong argument to change NEO tombstone for a 'regular' MFB.&nbsp; We have our eyes on MFB4 to mount on NEO but dependent on what Harvard needs.

Patty at Caltech plans to use MFB to do multiplexing, but when is unknown.

Are there any holes in Methane Mound data, as they'll need MFB to fill.&nbsp; Unknown, but probably a back-burner for them.&nbsp; Currently we don't know what contribution the instrumentation is making to the variation in the data.&nbsp; Gut feel is that we have endpoints and needn't worry about explaining away all variations we see.&nbsp; These will be point for future work, made in the discussion.

&nbsp;*PLAN*:
* Get MFB back from Caltech and prep it for Harvard.
* We WILL be swapping NEO's tombstone for an MFB.

h4. +&nbsp;3.&nbsp; Cores+

1.&nbsp; Will place order for spares this week.

2.&nbsp; Repair Mack's hand

3.&nbsp; Must run standard curve with the few remaining arrays on Mack & Bruce

4.&nbsp; NEO needs checking out with necessary repairs and/or replacements

5.&nbsp; Finish Betty

6.&nbsp; Revalve Bruce?
* MOE and Neo will be in the Spring 2011 deployment (unless Betty is ready--she'll replace NEO)
* Bruce or Mack will be cold-test machines .&nbsp; One will go to WHOI.&nbsp;

h4. +4.&nbsp; Other issues:+

* &nbsp;Must inspect all McLane pucks.&nbsp; Rejects to get sent back.&nbsp; Also must clarify the finish the pucks have with Ivory.
* We have a hoard of pucks that still need engraving.
* We need more HV puck testing.&nbsp; This could occur with the cold testing--Roman and Elif to work on together.
* All CTD's being sent back for service and calibration.&nbsp; Question; do we add an O2 optode or Clark Cell to our older Deep CTD?&nbsp; The goal for Deep is JdF, so what will work best there?&nbsp; Shallow CTD's to be sent out before Christmas.&nbsp; Need to decide about Deep CTD after the break.&nbsp; We have some time before the&nbsp; JdF cruise.
* Array Printer ;&nbsp; It WORKS\!&nbsp; Priority will be HAB arrays.&nbsp; We need to block out time for \~150 arrays for WHOI and then ours.&nbsp; Can print max of 64/day.&nbsp; Chris P working on getting new/different BAC probs for the BAC arrays we will also print.
* Roman would like to lead a HAB BioSpace Paper.&nbsp; These data are on Tornado but hasn't been parsed the way Roman and Chris do it.\\]]></property>
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<property name="body"><![CDATA[Present: Jim, Scott, Doug, John R., Julie, Bruce K., Chris S. Roman, Brent, John R.

Absent: Chris P, Elif (both CANON cruise)

h3. Issues:

* PUCKS
** Shana at Spyglass is a little behind in cleaning.&nbsp; We need LAF's and SH1's by Monday.&nbsp; Shana has&nbsp; been notified and will have everything by Friday (tomorrow).

* Does RNA-Later kill DA reagents?
** Tina and Greg have been working on this and do not think so.&nbsp; Even 1% solution (=strong) does not seem to inhibit the reaction.&nbsp; But they are testing under different atmospheric conditions than would be encountered in the can.&nbsp; Thus, needs can testing.&nbsp; {color:#6600ff}Chris S. to call Greg and talk about using/not using RNA-Later on the two BioSpace machines, which would provide and in situ empirical test of this hypothesis.{color}

* BIOSPACE DEPLOYMENT.
** Much discussion about getting water for Vanessa and how we can collect samples for her.&nbsp; Looks like Zephyr will get to M0 twice/day, so arrangements will not be difficult.&nbsp;
** There is the potential we can deploy all 3 machines in one day.&nbsp; {color:#6600ff}Scott to talk to Kim R. and Eric about this; also will check with Aaron when Zephyr returns.{color}
** We have batteries, and Paul setting up for box preparation.
** Moe at M0, Bruce at Santa Cruz, Mack in bight.
** Bruce and Moe get canned MONDAY.&nbsp; Radio check then; if problems, Brent in Tuesday to fix.
** LISST mounting on Bruce under CTD.
** Monday bases get set up in high-bay.
** Waiting to hear from Chris P on whether a post-QC run is necessary; we need to get the archives out and stored.
* ISMS
** ISMS will be on MARS deployment Nov 30, 2010.
** We plan on Pete doing development to take 48V power.
** Scott working on mounting web-relay switch.

* D-ESP
** IEP issues.&nbsp; {color:#6600ff}Doug ordering new type of piston IEP pump.&nbsp;{color} Waiting on PO approval.
** Needs to be mechanical adjustment of Gordon's elevator.&nbsp; too close to bottom of SC.
** {color:#ff0000}Sphere will be closed NOV 17{color} for Nov 30 deployment.
*** Much discussion over power requirements for D-ESP on Juan de Fuca next summer.&nbsp; Powering ISMS causing concern.&nbsp; Following are options:
**** get ISMS to power cycle, so it's only 'on' while taking a reading
**** develop new, lower power ISMS (Harvard would do this)
**** have additional battery elevator that would allow battery swapping and recharging on deck.
**** ISMS rides on and is powered by the ROV
**** ISMS carries its own power (Li?).
*** If no ISMS on D-ESP, charging would be greatly shortened, freeing up ROV for other operations.
*** If ISMS on elevator and using D-ESP power, worry is that bad weather, for instance, causes us to leave, and the ISMS will suck batteries dry, killing entire experiment.
*** This will get extensive discussion at AGU when we meet with Pete.

* Clamp re-design
** all parts are in and we can start testing at any time.
** currently will run puck evac at lower pressure and see if there are dribbles.&nbsp; This seems most conservative solution, not requiring hardware and minimal software change.

* WHOI spring deployment

** many, many unknowns about their deployment strategy.&nbsp; Gumby hose to pump surface water down to ESP, as well as surface expression (is it a mooring controller?) and radio comms to shore are all still under development.
** {color:#6600ff}Chris S. to call Don and let him know these issues potentially jeopardize the entire mission{color}.
** Will also check to see whether EOM guys are coming&nbsp; to visit MBARI.

* CTD--Bob Herlien has found the smoking gun in the newer firmware of the CTD's.&nbsp; He will train our software to ignore, and must back test against earlier versions of the CTD.&nbsp; That should be finished next week.

h5. +Machines+


h6. Bruce

Problem seems to be solved; have repaired the finger temp sensor.&nbsp; 3 good DA runs so far.

h6. Mack

Was deployed around 12:30pm on Sep 14.&nbsp; Glitch at beginning so did not start its mission until 6pm.&nbsp; Drifter moving SSW \~20cm/sec.&nbsp; Discovered that Drifter data not being logged internally; must have radio contact to see data.

h6. MOE

Vanessa re-running standards over the weekend.&nbsp; Both MOE and Bruce to be canned Monday.


h6.

finally...

The Logo for the ESP group has been selected and can be seen [HERE|^esp_eps.eps|New ESP Logo].\\]]></property>
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<property name="body"><![CDATA[Present:&nbsp;&nbsp; Vanessa, Jim, Roman, Bill U., Chris S., Scott, Brent, John R., Chris P., Doug, Elif, Liz O.
Absent: Julie

{color:#3300ff}1. Items:{color}\\
* {color:#3300ff}BioSpace Deployment{color}
** {color:#000000}Message from Aaron (Zephyr skipper) was he'd like to do 3 in one day.&nbsp; This crowds the boat and is not ideal, but we may go with this if we have divers.&nbsp; Still planning....{color}
** {color:#000000}Precruise has crew being Roman, Scott, Vanessa, Bruce K.{color}
** &nbsp;BRUCE : Offshore site (SC), 52m water depth, with saline EtOH and LISST
** MACK: Latmix site, 19m water depth, with RNALater
** MOE:&nbsp; M0 site, 72m water depth, ISUS
** will shoot to put all instruments at 7m below surface.
** Radios.&nbsp; Still to be checked.&nbsp; Brent to download all files off shore stations to clear up space.

* {color:#3300ff}D-ESP Plan{color}
** New IEP pump to arrive by end of week.&nbsp; Doug has \~3.5 weeks to install, test, and checkout.
** Plan is to load reagents Oct 21.&nbsp; From then on the ball should be kept at 16C, which means van at 10C w/ sphere heater on.
** Plan is to try and run 3 full phases as a checkout.
** Sphere is closed Nov 17.

h4. Other items

Chris P. leaving for vacation tomorrow.&nbsp; Returns Oct 4.
Scott on vacation Oct 4-20.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Brent, Scott, Doug, Jim, Chris S.


h2. Items:

+D-ESP+\\
# Batteries are now charged after its miraculous recovery.&nbsp; Drawing 2amps.&nbsp; Usually draws 1 to 2, but we will move ahead.&nbsp; Current limit on MARS now set for 15A (D-ESP peaked at 10.5A before death).
# Do we turn on ISMS?&nbsp; After discussion, we will let D-ESP run a phase, then turn on ISMS (which could be late tomorrow or next week).&nbsp; Potential recovery day Jan 2, 3, or 4.
# Chris P. should make her 'water request' to the Lobos. \\

+Surface+
# Scott has met with ROV pilots and handed off the design and building of the battery sled to them.&nbsp; Will order 1 more ODI connector (for a total of 4) so we have a spare.

* h3. Announcements

* Scott and Jim will attend one day of exhibits at ALA Jan 29.&nbsp; Will get Cindy to work out logistics.
* Jim meeting Pete Girguis at AGU next Weds.&nbsp; Given that the fundamental question of the JdF cruise is how it might provide a window into microbial populations given certain environmental conditions, what are the details we need from him?&nbsp; Suggestions:
*** Possible locations?&nbsp; Go to most important first.
*** Temperatures and depths?
*** Mass Spec
**** Can it be turned off and on to run again?
**** What power cycling scheme is possible?
**** How will/how much power reduction will we have by JdF?
**** What are defaults if we can't move the D-ESP given a top speed of 0.2knts while ROV is under water at depth.
*** Issues from Chris P:
**** Capture probes and frozen cells for the bacterioplakton he wants detect on the array.&nbsp; Sooner the better. I'll be starting testing of some new deep captures in early Jan. and can fold his in
**** We have to have in OUR hands his assay condition, primers and probes for loading on Gordon on April 25.]]></property>
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<property name="body"><![CDATA[Present:&nbsp;&nbsp; Jim, Scott, Doug, John R., Julie, Vanessa


Absent: Brent, Roman, Chris S. (England), Chris P, Elif (both CANON cruise)

h3. Announcements:

1.&nbsp; Chris Melancon has announced another pending order for an ESP.&nbsp; This is a NOAA contract and willgo to the NW Fisheries Science Center in Seattle, WA.

2.&nbsp; Audio track for the D-ESP YouTube movie will be recorded next week.&nbsp; Linda Kuhnz on vacation for 2 weeks but will have movie finished soon after her return.\\

This was&nbsp; short week due to Labor Day (Monday) and an off Friday.


h3. Issues:

* Julie ran full-phase through MOE last night with no glitches.&nbsp; She hopes to have MOE canned for BioSpace on Sep 15; she leaves for vacation Sep 16-Oct10.&nbsp;&nbsp;

* ISUS
** D-ESP:&nbsp; Luke has a Vicor power supply we can use; we've order him a replacement.
** NEO: ISUS will be given to John for refurbish and readiness for BioSpace.

* BioSpace ESP deployment is Sep 28, 29.&nbsp; Three machines:&nbsp; MOE w/PCR at M0.&nbsp; Bruce and Mack, both running only HAB, HAB/DA will be in the shadow and the bight.&nbsp; Which/where to be decided next week.&nbsp; Will work with Aaron from Zephyr when they return from CANON to decide how they'd like to do the deployments.&nbsp; LISST machine to go on the mooring that deploys in the shadow.&nbsp;

h5. +Machines+


h6. Bruce

waiting for Roman.


h6. Mack

is on the WF.&nbsp; they shoved off today at 10:30am for the beginning of the CANON cruise.&nbsp; All ESP systems are a-go\!


h6. MOE

Julie has run full-phase, and will run another tonight.&nbsp; No problems.

h6. Gordon

Still in the ball.&nbsp; After checking with Chris P, we have turned off van chiller.


h6. Betty

will be first to get the new, stiffer springs for clamp testing.]]></property>
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Present:&nbsp;&nbsp; Jim, Scott, Doug, Brent, Chris P., Chris S., Julie

Absent: Roman

h3. Announcements:

1.&nbsp; Elif Demir has joined the ESP team for 6 months.&nbsp; Welcome.

2.&nbsp; Custom Array (Combimetrix) coming tomorrow to talk about collaboration.

3.&nbsp; ESP logo competition begun.&nbsp; We will receive entries until Sep 10.&nbsp; Meet Sep 14 to decide winner.


h3. Issues:

* Pressure issues on all cores.
** Chris brought up issue that the sampling issue never gave us a problem before, now we're seeing it.&nbsp; Doesn't make sense.&nbsp; We think we have been dancing on the edge of accpetablility and have now crossed over (?) .&nbsp; Will continue to retro-fit cores with stiffer springs, and adjust the pressures reached to insure pucks don't pop open when pumped up.

* Antenna at Abe's
** Brent oversaw the mounting ($266.00) and antenna is working beautifully.&nbsp; Brent will turn down the power to 250mW (right now running at 1W) to give us a 4W effective.

* Drifter
** must have mission checkd.&nbsp; Chris S. will look over.&nbsp; Loading pucks today.
** Tomorrow is a comms check.&nbsp;&nbsp; QC check tomorrow.&nbsp; then power down and sit over the weekend.
** CANON cruise leaves Sep 9.&nbsp; Drifter deploys Sep 15.

* ISUS Pressure housing
** some minor changes (MINK fitting and vent port), then sending out for bid.

* DESP
** Doug working on an IEP replacement.&nbsp; He's testing new configurations, but there is potential problem with encoder.

h5. +Machines+


h6. Bruce

pressure test inconclusive.&nbsp; Going to run phase with Roman to see it that gives a clue.


h6. Mack

see Drifter above.


h6. MOE

Vanessa ran her standards this week.&nbsp; Julie to run a full-phase to check the new code added.


h6. NEO

is uncanned.&nbsp; CC is salty.&nbsp; Found liquid at bottom of housing.&nbsp; Think it's waste container overflow.


h6. Gordon

Still in the ball.

h6. Betty

no report.]]></property>
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<property name="body"><![CDATA[Present:&nbsp;&nbsp; Vanessa, Julie, Bruce K., Roman, Jim
Absent: John R., Chris P, Chris S.

{color:#3300ff}1. Items:{color}\\
* {color:#3300ff}BioSpace Deployment{color}
** {color:#000000}Set for Sep 28 & 29.&nbsp; Most likely MOE will go to M0 on 28th, BRUCE and MACK to other two sites on 29th.{color}
** {color:#000000}Crew not yet set, but Roman will lead deployments.&nbsp; Bruce K. will attend.&nbsp; Will decide the third.&nbsp; Bruce checking to see if anyone from EOM (Don Peters \[eng.\] or Mark Lambton \[PM\] might be here to attend the deployment.{color}

* {color:#3300ff}Moe issues{color}
** Julie has had some trouble with IPC on the MFB;&nbsp; it's internally consistent in it's Ct, but Ct's are different depending on if sample is run through the core or stand-alone.&nbsp; Julie has been hammering on this problem with advice from Chris P (on the WF Canon cruise).&nbsp; Might be a bad pull from PP1 pigtail, which has been replaced.&nbsp; She is also trying a 'better' IPC mixture.
** Julie will continue to work on getting the instrument working; she leaves on a trip Thursday PM, and should not worry about canning, as we'll take care that issue.

* {color:#3300ff}Bruce{color}
** Roman saw that Bruce failed the short DA yesterday, but discovered the puck heater was too hot to touch.  Seems to be a temperature feedback issue.  Will investigate with Scott today.

h5. Missions for Biospace

* From Aug 9, Roman had notes stating we'd run 15 HAB/DA, 4 Bac, 3 Larv.
* julie/vanessa setting up Moe.
* all mission plans to be finished by Friday (17th) for discussion next Tuesday.
* Jim will contact Spyglass to find out where they are with the new puck cleaning.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris P, Elif, John R., Roman, Allison, Bill, Chris, Jim, Julie

h2. &nbsp;Items Discussed:


h4.


h4. +1.&nbsp; Cold testing+

* Viscometer to arrive late this week
* Standard to arrive today.
* Testing Idea:

# Building of matrix has begun.
# using Wash Buffer with added methanol:

Test Matrix:
|| Temperature || || wash/block alcohol %by v/v \\ || || ||
| room | 0% | 5% | 10% | 15% \\ | 20% \\ |
| 10 | 0% | 5% | 10% | 15% | 20% |
| 4 (or \~2) | 0% | 5% | 10% | 15% | 20% |
* Will look at differences qualitatively, then
* collect viscometer data, then
* test on plates, then move to cold instrument.
* &nbsp;
* Chris P. working on SPEdil cold testing.&nbsp; Looks like there are minor changes in pH, depending on precipitation, but unclear if these will have any effect on assay.&nbsp; She will run PCR with calf thymus and various precipitated SPEdil and see if there is any change.

h4. +2.&nbsp; MFB Plans+

* Patty has shipped MFB9 back from Caltech
* Chris P will work on preparing that for Harvard

h4.


h4. +4.&nbsp; Other issues:+

* &nbsp;Will ship McLane pucks back today. Will include some of ours as samples for their machinist.
* Jim will figure out where the next numbering of pucks should begin, for the pucks still to be etched.

Julie presented her results from 2009 field work.

Bill presented his AGU poster. ]]></property>
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<property name="body"><![CDATA[This is the documentation to detail out the design of the state representation interface between the GUI application and the instrument itself.  This interface will allow the GUI (and other applications) to get information about the current state of the various components of the ESP.

Some details about the interface:
# The ESP application (server) shall listen on a fixed TCP socket.
# Any number clients can connect to this socket, each thereby opening a separate, private, bidirectional, ASCII connection to the ESP server.
# The server will respond to the following client commands:
## List all available states
### Each state is identified by a short symbolic (ASCII) name.
## Retrieve metadata for subset of those states and subscribe to them
### Elements in lists of states are separated with commas
#### There is no whitespace between list elements
### The order of the elements in state lists determine the ordering in reporting state vectors described below.
### Metadata shall include:
#### Description  e.g.  Storage carousel
#### sprintf format string  e.g.  %.2fml
#### range  (min and max expected values)
{note}hardware failures may cause reported values to be out of range
{note}
#### map of sybolically labeled positions, each on a line of this format:
{noformat}
  <numeric position>,<symbolic label>,<alias1>,<alias2>,<aliasN>
{noformat}
## Subscribe to updates on (only) the specified states
{note}This limits subsequent state updates to just those listed by their symbolic names. This message also determines the ordering of states in vectors described below.
{note}
## Refresh all subscribed states
{note}All the subscribed states are sent to the client in the order in which they were listed in the most recent subscribe or retrieve metadata message.
{noformat}
<timestamp?  seconds since epoch??>
<new value[0]>{,optional additional info like current, pwm%, etc. (may be ignored)}
<new value[1]>{,optional additional info like current, pwm%, etc.}
...
<new value[n-1]>{,optional additional info like current, pwm%, etc.}
{noformat}
where n is the number of states subscribed.  This establishes a baseline from which subsequent state changes are reported.
{note}
## Request C more changed state updates at maximum rate one per t tenths of seconds.
{note}
* The client tells the server it is ready to receive C more state change responses and that the server may emit these at a rate no faster than one every t tenths of a second.
* A client wishing to continuously monitor state should send a new request shortly *before* the last update (as allowed by the previous request) has been received. If C is kept small (say 10 or so), this mechanism will ensure that update messages don't back up on the networking queue, while avoiding paying any network latency penalty.  (Similar to TCP's sliding window mechanism)
* The client can stop updates by requesting 0 more at some arbitrary rate.
* Only those states whose values changed since the last update will be sent
* Format will be a list of lines, each of the form:
{noformat}
<index>,<new value>{,optional additional info like current, pwm%, etc.}
{noformat}
where:
* index = an integer from 0 to n-1 where n is the number of subscribed states
* new value = number conforming to the state's sprintf format string (note that the unit suffix will be omitted, i.e. 0.2 not 0.2ml)
{note}
{note:title=Notes for Brent}Normally, all I2C messages between the Linux host and the dwarves are logged. However, this protocol will require continuous polling of all the subscribed dwarves' raw positions.  Nothing else currently does anything like this (by design\! :-) . Clearly, such messages should not be logged.  Further, it may be necessary to add an I2C message to the dwarf firmware that queries raw position only.  The existing full status poll message returns lots of extraneous engineering info like velocity, electrical current, etc.
{note}]]></property>
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<property name="body"><![CDATA[For several aspects of the ESP GUI application, the application will have to have an associated user, which will, in turn, belongs to specifics groups.  The reason for this is that we do not want the application to allow any user to do all things in the ESP GUI.  For example:

# Maybe you want to limit users to read-only.
# Certain users can create mission scripts for certain ESP instrument
# Certain users can delete deployment information.
# etc.

In order to enable this type of access control, the Java SE security infrastructure was utilized in the GUI development.

Resources:

# [Java SE Security|http://www.oracle.com/technetwork/java/javase/tech/index-jsp-136007.html]
# [Java SE Security Overview|http://download.oracle.com/javase/7/docs/technotes/guides/security/overview/jsoverview.html]
# [JAAS Authentication Tutorial|http://download.oracle.com/javase/6/docs/technotes/guides/security/jaas/tutorials/GeneralAcnOnly.html]
# [JAAS Authorization Tutorial|http://download.oracle.com/javase/6/docs/technotes/guides/security/jaas/tutorials/GeneralAcnAndAzn.html]
# [JAAS Reference Guide|http://download.oracle.com/javase/6/docs/technotes/guides/security/jaas/JAASRefGuide.html]
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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Doug, Wayne, Cheri, Chris S.
Absent:&nbsp;&nbsp; Scott, Addie (maternity)

h3. Machine Builds

* Ivory from McLane arrives Monday for final week of ESP core assembly.
* modification on high-volume puck are finished.&nbsp; Doug has turned over to Chris and they are now waiting to be tested.
* Must order more scintered frits.&nbsp; Jim will take care of.
* PUCK ETCHING
** Brent has info from a company for bar-coding pucks.&nbsp; Jim can investigate.
** El Camino may be able to etch future pucks while in lathe.&nbsp; Check with Mike Parker.
** our next puck order will include many more high-volume pucks.&nbsp; We need an inventory of all pucks ; how many of what types?
** soon we will lose 2 cores: 1 to SC, 1 to WHOI, and each will take a set of pucks out of our inventory.

h3. MFB

* shop is slammed with work.&nbsp; Cheri coordinating with Mike about getting final 3 sets of MFB parts finished before shipping to McLane

h3. Software

* &nbsp;Brent has been able to scrounge cables and laptops.
* Ruby control of DWSM has begun
* NEO code vs. all other cores:
*** AIV valve: it's very easy to change ports on valves, but not easy to change what channel the valve is on.
*** Decision is to keep NEO in 'lab-mode' until Chris P gets through her testing, but then upgrade to make compliant with other cores.
* IRIDIUM modem on drifter.&nbsp; Is Gene using same modem as on MOOS?&nbsp; If so, no problem.
* dPress board review next weds @ 10am.

h3. DWSM


h6. +Sphere+

* &nbsp;Still in parking deck.&nbsp; Will be moved to tin-shed by facilities people.
* &nbsp;Doug to look into purchase of a (folding?) engine hoist for moving stuff within the van.
* Doug has designed center spider hanger cage for holding ESP core within the sphere.&nbsp; Parts to get to the shop today.

h6. +Elevator+

* &nbsp;We've decided the modem to purchase (w/ deckbox).&nbsp; Will cost $27K.&nbsp; Will charge to 900915.99.&nbsp; 10-week lead time, although this isn't needed until June.
* Because of g-loads during a drop, Doug has done some mod's to the design and will work on some Jeep-Bumper-like landing feet.
* Foam coming in tomorrow or early next week.&nbsp; Will be machined down the street at a boat shop(?)
* We need an ESP stencil to mark the foam

*{+}DWSM{+}*
* Bad pump has been sent back and will be repaired/replaced.
* Scott/Doug discovered they can't get enough power through the motor controller
** might got to two power supplies in series
** Scott working on board to make this work
** Brent should be cc'd on all this correspondence.
* Doug predicts that they should be pushing water and oil by middle of next week.

h3. Other Items:

* &nbsp;Refrigerated van has been ordered and will arrive next Tues/Weds (Feb 24/25).&nbsp; Call had gone in to Greg Voogd about setting up electrical hook-up.&nbsp; We will wait for Danny Day to do wiring, using extension cords if necessary for lighting.&nbsp; Once van here, we'll convene on where wiring/lights should be installed.
* Chris S. wants a NASA sticker on the side of the van
* Science deployment on Zephyr, April 1.
*** Will deploy BRUCE
*** Team will be:&nbsp; Roman M: lead, Chris P: scripts & mission planning, John Ryan: ISUS, Cheri and Wayne will work comms and mooring mechanics, Jose: batteries.
*** Before this deployment, we will switch over to&nbsp; locked version of the new code.&nbsp; Recently Bruce has been run with new code (off the network), but still has last deployment code locally.&nbsp; Brent will today load new code on locally, so much exercise can occur before April 1 deployment.
* Self-organizing TWIC teams are forming.&nbsp; Wayne, Chris S, and Scott are going up together.
* Teams need to be decided for two Flyer deployments:&nbsp; June 5-9 and Aug 15-27.&nbsp; Look at ship schedules to get exact dates.&nbsp; We want to arrive the day before the MOB day, and figure on returning home the day after reaching port.]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
\\
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage taken by Rob Vincent:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]

Map of locations:&nbsp; [http://maps.google.com/maps/ms?ie=UTF&msa=0&msid=213220825771739778963.0004a40bdd601babc291d]

May 23.&nbsp; Attempted recovery of ESP.&nbsp; Message from Roman:

{color:#996600}&nbsp;&nbsp;&nbsp; We went out to the site where espbruce was moored and attempted to find it.&nbsp; The weather was very poor and water was very turbid.&nbsp; Using the ships depth finder we found a promising target.&nbsp; In difficult conditions the divers performed a search but espbruce was not found.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; We recovered the mooring.&nbsp; It looks like the cable was pulled straight out of the cone.&nbsp; The top mast is bent but I cannot say if this was caused by a rough landing on the beach or boat impact.&nbsp; There are no dents or gouges on the mooring.&nbsp; The radio box is dry and antenna looks ok.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; Thursday the RV Gulf Challenger may be able to survey the area with a side scanning sonar.&nbsp; This will be a much better way to search for espbruce.&nbsp;{color}

Message from Roman May 26:

{color:#996600}&nbsp;&nbsp;&nbsp; ESPbruce was located at&nbsp; 43° 02.0740 N&nbsp;&nbsp; 70° 36.8447 W at ~ 10m depth.&nbsp; This position is about 19 yards from the waypoint.&nbsp; So looks like it wasn't dragged and has maintained seal integrity.&nbsp; We will attempt to recover it this weekend if we can get the RV Tioga.&nbsp; If not will recover with the RV Connecticut on june 7th weather permitting.{color}
&nbsp;

Dates for a recovery kept moving as weather and scheduling problems arose.&nbsp; Finally, Roman reported on June 15:
{quote}
{quote}
{color:#996600}ESPbruce was recovered today with no visible external damage. The EM cable strain relief is still on the cable.&nbsp; The recovery operation used two ships the RV Gulf Challenger and it's sister the RV Tioga.&nbsp; The Challenger supported the the side scan survey and the Tioga supported the divers and lifting of the core package and its anchor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;The side scan sonar operator advised me at the beginning of the day that he believed the esp package would be found on the bottom.&nbsp; He based this opinion on the data secured by his colleague almost two weeks ago.&nbsp; From his read of that run, he believed that the instrument was 15m off the bottom at that time.&nbsp; Depth at this site is 49m.&nbsp; He felt that the instrument was slowly sinking and that by today it was surly be on the sea floor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Todays side scan survey took approximately 90 minutes.&nbsp; They had acquired a strong signature on the core and calculated that it was at a depth of 65 feet (~20m). The package&nbsp; was still located within 10m of the original deployment site.&nbsp; They dropped a marker line with a float as close to the calculated position as possible.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;At this point divers equipped with twin 80 cu ft Nitrox cylinders and electric scooters dived on the marker.&nbsp; They had 70 minutes of search time.&nbsp; After 42 minutes an orange sausage float attached to a spectra lift line appeared.&nbsp; Then 10 minutes later a second lift bag attached to the EM cable appeared.&nbsp; The divers surfaced after a total bottom time of 62 minutes.&nbsp; Eight minutes to spare.&nbsp; We recovered the divers.&nbsp; They reported that the depth of top of the can was at 26 feet (~8m) right where it was supposed to be.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Recovery went smoothly using a single winch equipped with a capstan attachment.&nbsp; By alternately shifting the load from drum (used to lift anchor) and capstan (used to lift instrument we recovered the package and the anchor safely.{color}
{quote}
\\
\\  {color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford.

{color:#cc3300}July 6{color} \-\- Ship by truck D-ESP and supplies for JdF cruise.&nbsp; To Newport, OR.

{color:#cc3300}July 13{color} \-\- Sail for Axial and JdF (1 day late due to weather getting up to Newport)

{color:#cc0000}July 20{color} \-\- recall D-ESP.&nbsp; Recover all instruments.&nbsp; Two more days for Dave Clague.&nbsp; Ship returns July 23.
\\

Aug 17 \-\- Matson picks up loaded ESP van.&nbsp; Genset on truck putting out >530V so our reefer unit will not start.&nbsp; Decide to send due to late hour and ship leaving tomorrow.&nbsp; Van wt. w/ all ESP-Drifter gear: 15,000 lbs.

Sep 9 \-\- Drifting ESP deployed from Kilo Moana N of Station Aloha.&nbsp; Running Bruce w/ MFB ?.

Sep 17 \-\- Drifting ESP recovered.&nbsp; Gear shipped Oct 7 (via DHX and Matson), arrived at MBARI Oct 12..

{color:#9900cc}Nov 2{color} \-\- Install ESP Gordon w/PCR on Santa Cruz Pier.&nbsp; no CTD/ISUS data.&nbsp; Running water quality assay Kevan Yamahara developed.

{color:#9900cc}Dec 19{color} \-\- Recover from Santa Cruz Pier ]]></property>
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# [2011 Engineering Meetings]
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<property name="body"><![CDATA[h2. Engineering meeting


h4. &nbsp;Items:

* &nbsp;In 2011, we may swap a Zephyr day (May 19) to later and use Shana Rae on the 19th.
* Much discussion about the ship schedule in 2011.

Teledyne may become more involved in the engineering process with G3.&nbsp; We will get an NDA and MOU in&nbsp; place and possible host them at a mid/late Jan/Feb meeting.&nbsp; Chris going to visit them and see if they are interested in participating.
\\

h5. +G3+

* &nbsp;A system level diagram showing concepts needed.
* We should start from G2; e.g., 40 samples over 3 weeks would be a good minimum
* what about looking at sampling workshop output for sampling requirements?&nbsp; Chris S. will look to John R. to get this together.&nbsp; See what potential users want to do.

h5. +MARS+

&nbsp;We may move the recovery day from Jan 31to later in that week.

Adaptive SamplingWe will run the algorithm on shore and then push the 'decision' to the instrument.&nbsp; Brent to work on it this deployment.

Maybe use temperature as signal ;&nbsp; 3 runs when temp drops, 3 when temp rises, 3 when mid temp.&nbsp; Should stay simple if code is not ready

We need to retain 8 samples in reserve for this.&nbsp; Terminate mission the end of the first week of Jan.
Must push a patch down to DWSM as we think a compliance&nbsp; bag is broken.

h5. +&nbsp;G2+

Super-Clamp is on only Gordon right now.&nbsp; We have coaxial alignment pieces, but still need springs.&nbsp; Doug to order. ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Doug, Wayne, Cheri, Chris S., Scott, Gene
Absent:&nbsp; Addie (maternity)

h3. Machine Builds

* &nbsp;Gordon and Betty
** hand builds;&nbsp; modifications are in the shop but not an official shop work order
** some parts simply made incorrectly (El Camiino)
** Cheri will put into system today and we will prioritize
* Shallow lids
** simply use different port on lid so no modification needed.
** will use old power hole for Gene's pressure transducer
** Bottom line:&nbsp; No new hole in lids.&nbsp; Doug looking into whether there is a seal available.
* Light Puck
** The Phase config file was to be machine independent.&nbsp; But now we're seeing differences in cameras, so Brent's putting a machine-specific 'multiplier' into the phase config that references each individual camera.
** In the light puck vs. matched-array comparison, results are difficult to interpret.&nbsp; Will be using matched-array results so we will have instrument-specific calibrations--not ideal.&nbsp; For the moment, every machine has its own calibration & we'll multiply to make them the 'same'.&nbsp; Eventually the calibration will be empirically derived.
* Bruce is out of focus.&nbsp; Will not touch until after April 1 deployment.

h3. MFB

* MFB's to ship to McLane this PM.&nbsp; Will ship without PCR tubing.

h3. Drifter

* Design review today at 1:30 to discuss issues that may impact the foam design
* 1st test deployment is May 14.
* Must mount in ESP can:&nbsp; pressure transducer, accelerometer, serial->ethernet, ethernet hub and extender.&nbsp; Gene to work with Scott and Doug on this.
* Top-side
** Cable goes to slip-ring \-> eventually to host board that'll talk to Iridium modem.&nbsp; Host boards on top will need DHCP-otherwise we need to assign static IP addresses
** Gene has found that modems are soon to be obsolete--Dec 2009.&nbsp; $1750 ea/ we need 2.&nbsp;&nbsp; Gene looking into buying new vs. old.&nbsp; We could simply borrow one for test deployments.
** Brent wants to get old phone modems to do testing that will exercise our software.
** Plan is to use lead-acid batteries in plastic pipe.&nbsp; This setup is putting off the ultimate alkaline battery pack build.
** NEXT meeting will update on fitting stuff into core.

h3. Software

* &nbsp;dPress boards; still can't read registers.&nbsp; Wayne working on.
* Brent not started on DWSM yet.

h3. Deep ESP


h6. +Sphere+

* Spider construction.&nbsp; All parts are machine shop.&nbsp; Will be finished today.
* Frank F. will do welding week after next in the high-bay.&nbsp; We'll have to get the sphere bottom out of its crate for that.

h6. +Elevator+

* Foam should be ready March 15.
* Frame has been shipped to LA for heat treating.
* doug has ordered shock-load feet.

*{+}DWSM{+}*
* spider being welded today.&nbsp; sphere bottom is in machine shop.
* Power budget for modems not figured yet.&nbsp; this is critical path for June deployments, not earlier.
* interface boards ready next week.
* Big issue is high pressure pump:
** 2 pumps are bad:&nbsp; 1st is being repaired--stuck piston, 2nd showing same issues.&nbsp; Either too much air in it or debris.&nbsp; Doug waiting to hear from manufacturer on why they aren't working and he has some ideas for modifying pump.
** 1 bad motor--melted plastic inside, but then broke free; it now 'works', but is not trustworthy enough to deploy.
* Much discussion on whether we should have a timed or thermal time-out in software to shut pump down.&nbsp; {color:#cc0000}I was unclear what was decided.{color}

h3. Other Items:

* &nbsp;Van:&nbsp; not leveled yet.
* June cruise we hope to go to 2900m.&nbsp; Axial will be 1600-1800m.
* &nbsp;Will get Mack into cold-testing March 16.&nbsp; Do we switch syringes to cold-rated syringes?&nbsp; {color:#cc0000}I was unclear what was decided.{color}
* {color:#000000}GG will be core used to do sphere fitting, next week.{color}
* {color:#000000}Pfeiffer turbo pump will be serviced.&nbsp; Factory (not NST) calibration is fine.{color}
* {color:#000000}Chris S. pressuring Vrijenhoek on whether they want to use HV pucks.&nbsp; Chris will find out what Bob wants and how many.&nbsp;{color}
* {color:#000000}Scott will submit order for retainer rings.{color}]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Doug, Wayne, Cheri, Chris S., Scott
Absent:&nbsp; Addie (maternity)

h3. Machine Builds

* &nbsp;Cores:&nbsp; A big thanks to Cheri for all her hard work these last 4 weeks preparing and then leading the build effort while McLane was here.
** On Gordon and Betty:
*** all mechanical systems built, wired, and plumbed
*** all, that is, except the hands
*** discovered discrepencies on both Prunella and El Camino orders; some issues are the drawings, some are their work
*** we will be using one old, one new harmonic drive for the hands
** R-valves.&nbsp; 6 of 35 boards were bad.&nbsp; Dick had these marked in the Project Library, but Cheri didn't know about that spreadsheet.
* HV pucks.&nbsp; seems to be working well; got a nice array from 4L of fluid.&nbsp; If it works well for invertebrates, we might modify some of our SH1 pucks to test before we place a new puck order.&nbsp; Chris S. working on this.
* We need screens by end of April/May deployments.&nbsp; Science will inventory rings and screens so we can place new order.
* WAG:&nbsp; scope hardening of ESP to 200m = 1 year.
* &nbsp;



h3. MFB

* Mike has finished SPE heater modifications.&nbsp; Only need PCR tubing to ship to McLane.



h3. Software

* &nbsp;dPress code ready for testing.&nbsp; Wayne will load Monday AM
* Brent not started on DWSM yet.

h3. Deep ESP

* ISUS
** Luk says they have a 4km housing; just need a new probe--a PO away.&nbsp;
** We WILL NOT put ISUS on elevator in June
** John Ryan is taking over ISUS work.&nbsp; We may eventually want a TI housing.&nbsp; Craig Okuda may havve one for us (or a design)

h6. +Sphere+

* Spider construction.&nbsp; All parts are machine shop.&nbsp; Will be finished today.
* Frank F. will do welding week after next in the high-bay.&nbsp; We'll have to get the sphere bottom out of its crate for that.

h6. +Elevator+

* &nbsp;Still 3 weeks out.&nbsp; They had to send it out to be heat treated as their facility wasn't big enough.
* Modem.&nbsp; Because of where Clague will want to go while at Axial, we will probably NOT be within 2km of our drop site (which is required w/ a 60degree modem).&nbsp; Doug thinks we should change to low frequency modem--still working on power calculations, but seems we will buy a Low Freq omnidirectional model.
* Will purchase for the Flyer June deployment--must order in the next 2 weeks.
* Foam.&nbsp; being cut.&nbsp; ready in 2 weeks $1400.

*{+}DWSM{+}*
* Sample bags and switches are made
* We may not have stirrer motors in both bags by April.
* Bags are being assembled
* Oil & water not being pushed yet--still having Jose make interface boards--should be finished early next week.

h3. Other Items:

* &nbsp;Van:&nbsp; Doug has provided sketch of outlets (16) and lights to Greg Voogd
** we will push ESP to front of van and build a false wall so only front needs cooling
** Idea to put foldable desks (like Murphy tables)
** Need to check with Chris Grech about powering the van on UNOLS ships--what do we need?
** Greg will level the van next week.
** We need to figure out ventilation issues (i.e., false doors, screen doors, louvers, etc).&nbsp; Check w/ Ussler's van--how does he ventilate?
* Shallow ESP lids \--need modification.&nbsp; Original P1 connector is a threaded thing that is breaking.&nbsp; Needs re-machining.&nbsp; Scott will handle.
* Potential Institute-wide chemical inspection--should have MSDS for all chemicals in Bldg A & B labs.]]></property>
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<property name="body"><![CDATA[The goal of this work is to take the work done on the Java thick client GUI and make that same functionality available through a web application.

h3. Ruby on Rails

My first thought was that maybe I could point Ruby on Rails to the database that is being used by the GUI.  That would provide a nice integration with the Ruby that I would need to parse the log file and the database that contains all the information.  I tried doing this on the Mac, but had a heck of a time trying to get the Ruby on Rails to integrate with PostgreSQL.  Since we seem to be moving to PostgreSQL, I thought I would start to focus on this for the web application.  So, starting with a clean CentOS 6.2 VM, here are the steps I took:

1. ]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}MAKAI flight w 4 Archives, 1 Lyse-n-go{color}

*Feb 2-4, 2016*

Repeat of Dec flight.&nbsp; Here are notes from Yanwu's summary:

(Note: when reaching each target depth (peak-chl or pre-set), we give Makai 10 minutes to damp down depth undulation.)

Sample#1 (lyse&go sample. At chl peak):
Makai descended from surface, found the chl peak at 8.7m. On the ensuing ascent, Makai held depth at 8.7m, and triggered sample#1.
Took 63 minutes to complete.&nbsp; Then Makai surfaced to "report to shore".

Sample#2 (archive sample. At chl peak):
Makai descended from surface, found the chl peak at 12.7m. On the ensuing ascent, Makai held depth at 12.3m, and triggered sample#2. (Note: the water column was quite mixed vertically. The chl values at 8m and 12m were very close. Makai was doing her best to pick the relatively weak peak.)&nbsp; Took 41 minutes to complete.

Sample#3 (archive sample. At reacquired chl peak):
In order to reacquire the chl peak (considering the peak-chl layer may have moved up or down), Makai intentionally wiggled up and down (up first, then down, and then up). On the "down", it found the chl peak at 13.2m. On the ensuing "up", Makai held depth at 13.0m, and triggered sample#3.&nbsp; Took 40 minutes to complete.

Sample#4 (archive sample. At pre-set 27m. Control sample.):
Makai dove to the pre-set 27m depth, and triggered sample#4.&nbsp; Took 39 minutes to complete.

Sample#5 (archive sample. At pre-set 27m. Control sample.):
Makai stayed at the pre-set 27m depth, and triggered sample#5.&nbsp; Took 38 minutes to complete.

h4. {color:#ff00cc}Del Mar--ESP-Waldo{color}

*May 17, 2016*

Used M/V Merlin (Walt Crampton), with MBARI surface mooring.&nbsp; Divers from SCRIPPS.&nbsp; Deployed with CTD about 400 yds from Del Mar mooring (SE of their mooring). Used new anchor line, #1 shockle, and 35m EM cable.

Ship coordinates when we dropped it:&nbsp; 32' 55.603N&nbsp; 117' 18.895W
Melo coordinates (IMEI: 300034012090780):&nbsp; 32.92633 \-117.31491

Water depth 100m.&nbsp; Divers reported master link at 22.8m, can top at 16.76m.&nbsp; CTD reading \~18m.

Initial mission is to take a sample two hours after sunrise, every weekday.

*Nov 10, 2016*

Recovered ESP-Waldo.&nbsp; used M/V Merlin with Scripps divers.&nbsp; Drove home with 5'x9' trailer w/ramp using MBARI van #4.

h4.


h4. {color:#ff00cc}ESP-Moe;&nbsp; Moran in Monterey Bay{color}

*Sep 26, 2016*

After two-day wait for weather to settle, deployed ESP MOE at M0.&nbsp; No  mission loaded, as they wanted to manually fire each archive and have  more control over when they would manually collect samples.

Shana Rae used, with Charles Bock & Mike Conway diving.&nbsp; 15.6m EM cable with Shockle #2.&nbsp; CTD is around 5.65m deep.

Oct 7, lost comms to Moe.&nbsp; Modem and Cell provider check out.&nbsp;  Electrical signal up/down EM cable check out.&nbsp; Oct 11 bring out computer  to see if we can talk to can.&nbsp; no luck.

&nbsp;*Oct 13, 2016*

&nbsp;Got Shana Rae and divers (Eric + George) at the last minute.&nbsp; Weather beautiful. Flat.&nbsp; Recovered instrument on deck, and tried three ways to tunnel in to talk to host.&nbsp; No luck.&nbsp; Brought instrument home and could not communicate with host after uncanning.&nbsp; Scott traded carrier board with one in Brent's office and it worked.&nbsp; Moe carrier board did not work on another Sleepy.&nbsp; Work continues to discover why/ what went wrong on carrier board.

&nbsp;*Oct 27, 2016*

&nbsp;Got Shana Rae and divers (Jeff S and Paul C.).&nbsp;  Deployment went very smoothly.&nbsp; difficult cell phone reception at site.&nbsp; Got confirmation of depth (6.7m) and started home.&nbsp; After about 15 minutes got call from Brent that carousel was jammed and would not turn.&nbsp; Suggested recover.&nbsp; We returned and recovered and brought everything home.&nbsp; inspection showed that a carousel rod had unscrewed itself,fallen, and jammed against the elevator, freezing the carousel.&nbsp; Weather is turning more mercurial; will try to redeploy on Wed, Nov 2.
\\

*Nov 2, 2016* &nbsp;

Got Shana Rae and divers (Jeff S and Mike C).&nbsp; Deployment went smoothly, although had to wait for fueling of WF on dock.&nbsp; Left 11:30am, returned \~3pm.&nbsp; Depth 6.5m.&nbsp; This will be a 2-week run.

*Nov 17, 2016*

Textbook recovery of ESP-Moe, ending the Moran deployment.&nbsp; Used Shana Rae w/ divers, George & Kim R.&nbsp; Left dock at 8:20am, returned \~11:00.&nbsp; Some swell and coolish/cold.

h4. {color:#ff00cc}3G ESP in Monterey Bay{color}

*Dec 14-19, 2016*

Perform 5-cartridge depth/pressure testing in MB.&nbsp; Launched Makai with Honu; mission was to sample at chl max, 50m, 100m, 200m, and 300m.&nbsp; Sent vehicle up off Davenport to find deep enough (but not too deep) water for tests.

Results:

+Dec 15+

First cartridge fired \~8am at chl max (~14m) with avg chl 1.9ul/l.&nbsp; Took 45 minutes to sample 1L.

Second cartridge (50m) fired (~3:20pm) and took 57min.

Third cartridge (100m) fired (~6:36pm) and took 35min.

+Dec 16+

&nbsp;Difficult keeping on station, but started 200m cartridge \~8:27pm.&nbsp; Vehicle timeout caused vehicle to cut power to ESP after 60min, before ESP was finished sampling.

+Dec 17+

Difficulty finding 300m water within the vehicle timeouts.&nbsp; Vehicle dropped weight on a return to surface, as it thought it was taking too long. &nbsp; Also, Rowe (ADCP) caused a computer re-set just before sampling was to commence.&nbsp; Difficult day....

+Dec 18+

Turned off ADCP.&nbsp; In slightly deeper water and successfully fired off sample.&nbsp; Vehicle recovered next day.

Post-recovery summary by Chris Preston:

Upon startup in the lab, the PV could not reach home and pinned the SC. &nbsp;It did not properly home. This likely occurred during the sampling of the 300m sample. &nbsp;Cartridge summary to follow:[11:37]&nbsp;Cartridges run at 14m, 50m and 100m all sampled and preserved correctly. &nbsp;No indication of bubbles upon inspection. &nbsp;For these cartridges ran archiveEvac to clear out RNAlater in puck.
;
Cartridge run at 200m timed out before sampling completed. &nbsp;Did not get command from Makai to process the sample, thus it was not fixed. &nbsp;Back in the lab, ran archiveEvacAUV (full RNAlater fix procedure). &nbsp;No indication of bubbles introduced during sampling.
;
Cartridge run at 300m sampled for 15min correctly, Honu received commands from Makai to process. &nbsp;ESPhonu failed to actuate the PV and thus the sample was not preserved. &nbsp;Ran archiveEvacAUV. &nbsp;No indication of bubbles introduced during sampling. &nbsp;My best guess is that the carousel wasn't aligned properly and that the PV managed to get jammed upon actuation. This is the state that the instrument was in when it was brought to the lab.
;
So, Makai-ESPhonu sampled at all depths... 3/5 samples preserved.]]></property>
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<property name="body"><![CDATA[After working with the log files from a PCR run, it really challenged the way I was thinking about things.  I did a fairly substantial refactor (even if only in my head) and made things more shallow.  Most evertything is a ProcessRun now.]]></property>
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Cawthron Institute
98 Halifax St. East
Private Bag 2
Nelson 7042
New Zealand

Overall Shipper:
TNL--Auckland, NZ.  Christine Palmer (very unhelpful)
KSI--NZ Customs Agency

Sea Shipment
Lisa Parlier
Primary Freight Services
Rancho Dominguez, CA
310-635-3000 x243

Van Picked up March 19; deliver to Cawthron by April 25
20' ESP Van contained:

\**2 palletainers
\*1 ESP base with pressure housing can
\*1 buoy
\*1 He leak detector
\*1 orange lift table ]]></property>
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<property name="body"><![CDATA[Here are some links to information that was important during the design of the GUI:

h5. General Swing
# [A Visual Guide to Swing Components|http://java.sun.com/docs/books/tutorial/ui/features/components.html]
# [Laying Out Components Within a Container|http://java.sun.com/docs/books/tutorial/uiswing/layout/]
# [How to Use Split Panes|http://java.sun.com/docs/books/tutorial/uiswing/components/splitpane.html]
# [Threads and Swing|http://java.sun.com/products/jfc/tsc/articles/threads/threads1.html]

h5. JGoodies Forms
# [JGoodies Forms FAQ|https://forms.dev.java.net/faq.html]
# [The JGoodies Forms Framework (PDF)|http://www.jgoodies.com/articles/forms.pdf]
# [JGoodies Forms Tutorial - Introduction|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/introduction.html]
# [JGoodies Forms Tutorial - Basics|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/basics.html]
# [JGoodies Forms Tutorial - Quick Start|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/quickstart.html]
# [JGoodies Forms Tutorial - Building|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/building.html]
# [JGoodies Forms Tutorial - Factories|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/factories.html]
# [JGoodies Forms References|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/references.html]
# [JGoodies Forms Tips and Tricks|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tips.html]

h5. MiGCalendar
# [JavaBeans Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/JavaBeans%20Guide.pdf]
# [Getting Started Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Getting%20Started.pdf]
# [AShape Developers Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/AShape%20Developers%20Guide.pdf]
# [FAQ|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/FAQ.pdf]
# [MiG Calendar Tutorial (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/MiG%20Calendar%20Tutorial.pdf]
# [Running the Examples (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Runnig%20Examples.pdf]
# [Themes Developer's Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Themes%20Developers%20Guide.pdf]
# [JavaDocs|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/JavaDoc/index.html]

h5. Ruby/JRuby
# [Embedding JRuby|http://kenai.com/projects/jruby/pages/RedBridge]
# [Embedding JRuby - Code Examples |http://kenai.com/projects/jruby/pages/RedBridgeExamples]
# [Deploying JRuby with Java Web Start|http://www.infoq.com/articles/jruby-deployment-with-webstart]

h5. XTide
# [XTide Web Site|http://www.flaterco.com/xtide/]
# [A Brief Introduction to XTide|http://www.linuxjournal.com/article/196]]]></property>
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&nbsp;Present:&nbsp; Jim, Chris P, Chris S., Elif, Roman, Bill U.

h4. Items:

# WHOI deployment.
## Deploy April 20, flip June 4, recover July 20
## Elif has done much work with cold testing of reagents.&nbsp; Rejected methanol as an 'antifreeze' as viscosity increases with lowered temps.&nbsp; Will try adding buffer E to block and see if that helps.&nbsp; Also will try ethylene glycol which she ordered today.&nbsp; Must also test lysis buffer without SDS and see if it works similarly to&nbsp; present lysis buffer.
## tests will begin on the bench and move to the ESP.
# Standard curves
## Chris S. rethinking the efficacy of running standard curves when we don't really know the strength of the bugs being tested.&nbsp; Better to use a correction factor against Diane's old curves.
## Roman has much testing to do (linker, spacer) but printer is running well.
# ESP waste
## Phone conference with Kevin Creed tomorrow to discuss our waste generation and whether mixing our bleach solution with RNALater is a problem.
## Currently, all liquid and solid waste is identified as hazardous and disposed of appropriately.
## Results from our discussion will direct redesign of the next gen waste container.
# Bill has begun gathering logistics for the ESP cruise
## we may use the CTD
## will ship ESP in van, instead of transiting up on boat.
## Will have a cruise planning mtg next Monday, 9:30am with Girguis to discuss cruise logistics.
# Spring 2011 Monterey Bay deployment
## Chris Francis (Stanford) wanted to follow a deep deployment with a surface, and may be interested in adaptive sampling for nitrate loving bugs.

h5. Other items:

# &nbsp;ASTEP II planning mtg was tentative for Jan 25. Now moved to Feb 7, when Pete will be here at MBARI.
# Elif ready to number our remaining 'unnumbered' pucks.&nbsp; Must give her label series to begin with.
# Melancon bringing China visitors from Zealquest on Jan 19 in the PM.]]></property>
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\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] \- first discussion of adaptive sampling strategies
# Mar 3 - CMORE Hawaii
# [Mar 10] \-\- wand schematic
# [Mar 17]
# [Mar 24]
# Mar 31 - team deploying MOE at M0; Brent at WHOI
# [Apr 7]
# [Apr 14]
# [Apr 21]\--wand schematic reminder...
# [Apr 28]\--D-ESP 2-Year Birthday Celebration\!\!&nbsp; (Poster is [here|^ESP Birthday Poster(smaller).pdf])
# May 5 \-\- Visit to ASU
# [May 12]
# [May 19]
# [May 26]
# [Jun 2]
# Jun 9
# Jun 16
# [Jun 23]
# [Jun 30] \--Final prep before JdF
# Jul 7
# Jul 14
# Jul 21
# Jul 28
# [Aug 4]
# Aug 11
# Aug 18
# Aug 25
# Sep 1]]></property>
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# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]
# [Apr 12] \-\- Roman at WHOI, Chris P Europe
# Apr 19
# [Apr 26]
# [May 10]
# [May 17]
# May 24 \-\- Roman at WHOI, Chris S at WHOI, Chris P out
# [Jun 14] \-\- This has link to lysate dilution page
# [Jun 21]
# [Jun 28]
# Jul 5 \-\- MBARI closed
# [Jul 12] \-\- most of team at JdF
# Jul 19
# [Jul 26]
# [Aug 2]
# [Aug 9]
# Aug 16
# Aug 23
# Aug 30
# Sep 6 \--Joint Science/Engineering
# [Sep 13] \--Joint Science/Enginering]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Kevin G., Rich S., Chris P, Chris S, Roman, Gene, Doug, Bill, Elif, Jim, Scott, Brent


Items:
# Kevin gave an update on the GUI software, and invited users to a demo/discussion at next Weds software meeting.&nbsp; 11am in Surface.&nbsp; Rich also spoke with Brent about next steps in developing the machine visualization software.
# D-ESP.&nbsp; Currently in the van, hooked into the MARS simulator.&nbsp; DMO will need to run some tests for several days.&nbsp; Batteries on D-ESP will be charged by this PM.&nbsp; Science will discuss the runs available to us based on puck load remaining.
# Drifter
## CMORE cruise will be Oct 7-Oct 21, 2011.
## Gene presented high over-view of tasks and who on team would be most impacted (mostly Scott and Brent).&nbsp; Brent likely to take over comms issues.
## PAR and ADCP need work.&nbsp; John R. may take over spearheading this.
# NSF-OTIC
## Meeting is Jan 27
## Will have tele-con with Scott Soderburgh early next week for preliminary questions answered.
# WHOI deployment.&nbsp; April 20, flip June 4, recover July 20
## many exchanges with Bruce Keafer leading us to believe they are finally starting to see the difficulties with their mooring issue and timeline.
## Chris S. continues to ping on them for information on comms and deployment logisitics.&nbsp;
## We will be sending Roman out early, and probably Brent to do comms checkout.
# Juan de Fuca (July 12-24, 2011)
## Bill U handling logistics.&nbsp; Jim, Chris P., and Bill will tele-con with Pete Monday (9:30) for preliminary planning.
## Pete here at MBARI Feb 7 to give 2:15 seminar.&nbsp; Will hold ASTEP II review with Orphan's group that day.
# G3 disucussion
## Much discussed about where initial efforts should focus (instrument parts, or system level blocks).&nbsp; Consensus was to work both in parallel.&nbsp; Starting with filtration and folding that into the trade-space of the system with repeated iteration.]]></property>
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<property name="body"><![CDATA[h1. Engineering mtg

Present: Birch, Jensen, Pargett,  Preston, Gomes, Radochonski, Everlove
Absent: Scholin, Roman, Marin

h3. Issues

A.&nbsp; Spare Boards

* They are starting to arrive.&nbsp; Cheri noticed that testing rigs taken to McLane don't work for one of the tests with this latest version of Ruby.&nbsp; That test needs a little fiddling with the gains.&nbsp; She will work with Scott to fix that, then come up with a testing schedule that brings Paul Coenen into the loop to do some of this board check-out.

B.&nbsp; Benthos Deck Box

* Doug sent out an all-hands request to look for our missing deckbox.&nbsp; No response.&nbsp; We are checking with Benthos to make sure they shipped us the returned box, after we returned their loaner.&nbsp; Person to do that at Benthos is not in until Monday, so waiting.&nbsp;

C.&nbsp; Machine Blackout Covers

* We do not need anymore.&nbsp; McLane my, and Cheri will put the manufacturer in touch to see.&nbsp; Scott brought up point that covers are actually covering up a broken item.&nbsp; The light seal should work, but doesn't, so that's why we need the curtain.&nbsp; We should fix, but this item remains low priority.

D.&nbsp; ISMS
* it was finally delivered to Harvard, but it's unclear whether Girguis actually has it or not.&nbsp; Wayne sent plans, and they were supposed to re-do the wiring harness and get the instrument back to us by end of April.&nbsp; Looks doubtful.&nbsp; Wayne will be point of contact and also get dimensions of housing so Doug can start designing mounting hardware.

E.&nbsp; D-ESP
* Drop weight tested, is good, and can be mounted.
* New bulkhead valves are in
* pressure transducers will ship April 27
* Sample-side is back together and Doug has been testing it daily.&nbsp; It has yet to fail.
* will change gears and transducers when they come in, and be ready for Brent to tweak when he returns
* Have Bill Ussler as a 'featured speaker' at our April 20 Science meeting to discuss deployment on the methane mound.&nbsp; We may need to increase our sampling tube length (max of 15m).

F.&nbsp; Surface Can Lids
* Neo's current lid is populated from SC pier deployment; never been leak tested.
* Cheri will leak test and put older, leak tested lid from Moe onto NEO. ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Bill, Elif, Chris P, Chris S, Julie, Jim

h3. &nbsp;Items:

&nbsp;1.&nbsp; JdF
* Ball is literally in Doug's hands.&nbsp; He's building elevator.&nbsp; Several issues that we've applied band-aid fixes to...# 10m ODI cable has failed their testing and they are remanufacturing.&nbsp; Delivery date is on-or-before June 22.&nbsp; This will make it difficult to test connected to ROV.
# Doug has found ground fault b/w ball and frame (reads 2 ohms).&nbsp; Mitigate by lots of zincs and short deployment time (10 days).
# Carousel issues.&nbsp; Motor drawing far too much current and hot.&nbsp; Lubed carousel, loosened motor belt, milled home flag so no drag.&nbsp; Better, but still not like Moe.&nbsp; Decided to go with it.
# ISUS is two week late.&nbsp; Unable to test new cable from (new) pressure housing to ball, as we needed to close the sphere.
# Harvard's PCR assays do not work.
# CSV valve leaked in the b/w 6 and 7 position.&nbsp; Exchanged with Betty's; leaked again.&nbsp; Found third valve that didn't leak.&nbsp; Unable to completely test, but Gordon did pass the post-can QC runs.
2.&nbsp; Chris Preston's last day before JdF will be June 30.

3.&nbsp; Elif working on developing primers/probes for Pseud's.&nbsp; Has run into some contamination problems.&nbsp; Eventually we will need a lysate dilution step when going from core to MFB; We will get Chris P involved in that discussion along with Kevan Yamahara, possibly June 28. Chris has begun this [here|Lysate Dilution|lysate dilution ideas].


4.&nbsp; Several jobs developing for Nilo.&nbsp; Puck and Carboy cleaning.

5.&nbsp; ESP Drifter.
* Julie to start attending Tuesday's to discuss Drifter preparations.
** She has preliminary list of 'to-do's' (like a power budget)
** She will be getting Hawaii water on the 23rd, to see if we can filter 2L, and how well her p/p work.
** Currently going after 6 targets:&nbsp; IPC, Grp A, Grp B, Trichodesmium, Hetercystous, and a Synechococcus target ]]></property>
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<property name="body"><![CDATA[h3.


h3. This email discusses the changes that have to occur to have HAB arrays and qPCR from one sample event.&nbsp; It also incorporates the other possible code changes that have to occur on NEO.&nbsp; We should also keep in mind running the DA arrays in concert and how this affects the plumbing and valve moves of the PRV.

\\

1.&nbsp; Copy NEO's current Flash to Tornado

{color:#3300cc}6/14/11{color}&nbsp; Tornado/ESP/NEOtombstoneCode11jun14

2.&nbsp; Update code on NEO (Brent has already updated ruby code) and determine what is now "broken"

{color:#3300cc}6/14/11{color} moved to bufflehead.&nbsp; Use user preston.&nbsp; Problems with /var/log setup and the correct path for mounting bufflehead. If it loose home or fails use /sbin/service nfsmount start to regain connection.&nbsp; You must be a superuser.&nbsp; Brent will have to look at this when he returns.&nbsp;

3.&nbsp; Rig with Dummy MFB to make seeing core moves easier
4.&nbsp; Determine if the AIV lines (to PRV and CBV) need to be changed.
&nbsp;&nbsp; &nbsp;a.&nbsp; To match other instruments and handle the larger lysate volume generated by the HAB protocol

{color:#9933cc}6/15/11{color} With the current lines on NEO and new code only recover 700ul of lysate.&nbsp; Prime is not correct we loose too much. After CS.push to 0 the line between the PRV and PTV is completely filled with lysate which is all sent to waste.

5.&nbsp; Do we have enough lysate volume for delivery of 1ml lysate to the array and up to 250 ul for the qPCR?
&nbsp;&nbsp; &nbsp;a.&nbsp; update PRVprocess.rb to handing the priming of the larger volume (depending on length of CBV-AIV-PRV line this may effect the positioning of the lysate to the PRV for the bacSHAmfb protocol)
6.&nbsp; Update code to deliver 1ml lysate (undiluted ) to array.&nbsp; Current protocol dilutes to 1.5M GusCN for BAC array.
7.&nbsp; Create and testing of&nbsp; habSHAmfb protocol based on the structure of the bacSHAmfb
&nbsp;&nbsp; &nbsp;a.&nbsp; Start with "normal protocol"&nbsp; 250ul of lysate and 225 ul of SPEdiluent
8.&nbsp; Testing of dilution of Lysate protocol

{color:#3300cc}6/15/11&nbsp;{color} Dilution protocol will have to include a rinse of the mixloop.&nbsp; The transferPRV protocol uses the mixloop to depressurize the lines.&nbsp; Lots of concentrated lysate.
9.&nbsp; Timing of array hybridization with lysate dilution step \--incorporation into habSHAmfb and mfb protocol
&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-----update of bacSHAmfb is not necessary for Pier deployment
10.&nbsp; CC clamp has to get the heavier springs

h3. The second email Diluting Lysate for qPCR on ESP&nbsp; (Email 2 of 2)-\- is  exactly for that lysate dilution by the core prior to delivery to the  MFB.

Brent added code to pass in an optional block in the loadMFBslug protocol, which will make its implementation much easier.&nbsp; It will have to be determined if the timing of diluting the lysate fits into the current time alloted for the hybridization of the array (if one is being run on the same sample.)&nbsp; This code starts once the concentrated lysate has been primed to the PRV.

The Major steps are:

{color:#000000}0.5&nbsp; rinse of the mixloop (Add to beginning of dilution protocol before loadMFBslug starts){color}

1.&nbsp; Airs out mixloop line (Currently done in loadMFBslug)
2.&nbsp; Dilution of Lysate (start with 1:10 dilution).&nbsp; Pulls lysate 0.1 ml then GuSCN 0.9ml (1ml total volume), into PS via PRV-PSV line. Then fills the syringe with air from the PRV.&nbsp; Mixes the lysate.
3.&nbsp; Move the diluted lysate into mixing coil.
4.&nbsp; Rinses the PSV-PRV-AIV/CBV line, bypasses mixloop (created samplePassF--based on samplePassCa)
5.&nbsp; Moves diluted lysate held in mixing coil to the CBV-AIV line.&nbsp; Primed to PRV.valve
6.&nbsp; Mixes diluted lysate with speDil (same protocol/ratio in loadMFBslug)
7.&nbsp; Positions slug in AIV for MFB (completes loadMFBslug)

Possible Valve Configuration Change for PRV::
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; GuSCN has to be primed to valve
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; Assumes that we don't change current DA reagent positions.

A.&nbsp; With DA reagents
&nbsp;&nbsp;&nbsp; 1 AIV/CBV
&nbsp;&nbsp;&nbsp; 2 ab1
&nbsp;&nbsp;&nbsp; 3 speDil
&nbsp;&nbsp;&nbsp; 4 guscn
&nbsp;&nbsp;&nbsp; 5 Sipper // diluent?
&nbsp;&nbsp;&nbsp; 6 waste2
&nbsp;&nbsp;&nbsp; 7 ab2
&nbsp;&nbsp;&nbsp; 8 air clean
If BAC arrays are performed on samples also for qPCR, then the sipper has to be converted into diluent.

B.&nbsp; w/o DA reagents&nbsp; (Nearly same as current PRV valve with MFB attached)

{color:#0000ff}5/15/11 GuSCN is on PRV.3 Spare1:&nbsp; The valve configuration has not yet been altered.{color}


&nbsp;&nbsp;&nbsp; 1 AIV/CBV
&nbsp;&nbsp;&nbsp; 2 diluent
&nbsp;&nbsp;&nbsp; 3 guscn&nbsp; #was spare1
&nbsp;&nbsp;&nbsp; 4 spare2
&nbsp;&nbsp;&nbsp; 5 Sipper
&nbsp;&nbsp;&nbsp; 6 waste2
&nbsp;&nbsp;&nbsp; 7 spedil
&nbsp;&nbsp;&nbsp; 8 air clean

def diluteMFBlysate&nbsp; #apart of PRVprocess.rb
\# uses loadMFBslug above, but performs a dilution of the lysate for qPCR

\# CAN PARAMETERIZE THE DILUTION???---Comes much later. Ask Brent how...

\#Put in rinse of mixloop here. &nbsp;


loadMFBslug do
&nbsp; #Mixes lysate and GuSCN into syringe
&nbsp;&nbsp;&nbsp; Log.record "diluting Lysate in Syringe"
&nbsp;&nbsp;&nbsp; PSV.to :PTV
&nbsp;&nbsp;&nbsp; PTV.to :PRV
&nbsp;&nbsp;&nbsp; CBV.to :PRV
&nbsp;&nbsp;&nbsp; PRV.to :air
&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp; PRV.to CBV
&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp; PS.pull 0.1, PSslow
&nbsp;&nbsp;&nbsp; delay 5
&nbsp;&nbsp;&nbsp; PRV.to :guscn
&nbsp;&nbsp;&nbsp; PS.pull 0.9
&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp; PRV.air
&nbsp;&nbsp;&nbsp; PS.fill
&nbsp;&nbsp;&nbsp; delay 2

&nbsp; #Moves diluted lysate to PRV mixing coil
&nbsp; Log.record "Parking diluted lysate in Mixing Coil"
&nbsp;&nbsp;&nbsp; PSV.to :mixloop
&nbsp;&nbsp;&nbsp; PTV.to :PRVmixing
&nbsp;&nbsp;&nbsp; PRV.to :CBV
&nbsp;&nbsp;&nbsp; PS.push MixLoopPull&nbsp; #need to determine volume start with MixLoopPull
&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp; PSV.to waste1
&nbsp;&nbsp;&nbsp; &nbsp;PS.empty
&nbsp;&nbsp;&nbsp; &nbsp;PSV.to PTV
&nbsp;&nbsp;&nbsp; &nbsp;PTV.to PRV

&nbsp; #Rinses PRV-AIV-CBV line, bypasses mixloop
&nbsp; samplePassF

&nbsp; #Primes diluted lysate to PRV (CBV-AIV-line)
&nbsp; Log.record "moving diluted lysate into CBV-AIV line"
&nbsp;&nbsp;&nbsp; PSV.to :air
&nbsp;&nbsp;&nbsp; &nbsp;PS.fill
&nbsp;&nbsp;&nbsp; &nbsp;PSV.to :mixloop
&nbsp;&nbsp;&nbsp; &nbsp;PTV.to PRVmixing
&nbsp;&nbsp;&nbsp; &nbsp;PRV.to CBV
&nbsp;&nbsp;&nbsp; &nbsp;PS.push 0.9 PSslow
&nbsp;&nbsp;&nbsp; &nbsp;delay 2
&nbsp;&nbsp;&nbsp; &nbsp;PRV.waste2
&nbsp;&nbsp;&nbsp; &nbsp;PS.empty

&nbsp; #Mixes diluted lysate with speDil
&nbsp; Log.record "mixing lysate with speDil"
&nbsp;&nbsp;&nbsp;&nbsp; PSV.to :PML
&nbsp;&nbsp;&nbsp;&nbsp; CBV.to :PRV
&nbsp;&nbsp;&nbsp;&nbsp; PRV.to :air
&nbsp;&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp;&nbsp; PRV.to :speDil
&nbsp;&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp;&nbsp; PS.pull 0.225, PSslow
&nbsp;&nbsp;&nbsp;&nbsp; delay 5
&nbsp;&nbsp;&nbsp;&nbsp; PRV.to CBV
&nbsp;&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp;&nbsp; PS.pull .250, PSslow
&nbsp;&nbsp;&nbsp;&nbsp; delay 5
end
end

def samplePassF cleanCS = nil&nbsp; #In samplePass.rb
\#rinses PRV-AIV-CBV line, bypasses mixloop
\#run option (flush) block afterwords
\#also allows cleanCS protocol
&nbsp;Log.record "Beginning samplePassF"
&nbsp;CC.loadFlushPuck do
&nbsp;&nbsp; MFB.bypass if defined? MFB

&nbsp;&nbsp; #put 1.5ml of flush into PS
&nbsp;&nbsp; PSV.to PSR, :via=> :waste1
&nbsp;&nbsp; PSR.to :flush
&nbsp;&nbsp; PS.to 1.5
&nbsp;&nbsp; delay 5
&nbsp;&nbsp; PSV.to :waste1
&nbsp;&nbsp; PS.to 0
&nbsp;&nbsp; PSV.to PSR
&nbsp;&nbsp; PSR.to :air
&nbsp;&nbsp; PS.fill

&nbsp;&nbsp; #Backflush PRV - CBV line to CTV spit; bypasses mix loop

&nbsp;&nbsp; PRV.connect CBV
&nbsp;&nbsp; PSV.to :PTV, :via=> :air&nbsp;&nbsp; #Check this direction
&nbsp;&nbsp; CTV.to :air, :avoiding=>:intake
&nbsp;&nbsp; PTV.to :PRV
&nbsp;&nbsp; PS.to 0

&nbsp;&nbsp; #clear the line of fluid
&nbsp;&nbsp; PSV.to :air
&nbsp;&nbsp; PS.fill
&nbsp;&nbsp; PSV.to :PTV
&nbsp;&nbsp; PS.to 0
&nbsp;&nbsp; PSV.to :air
&nbsp;&nbsp; PS.fill
&nbsp;&nbsp; PSV.to :PTV
&nbsp;&nbsp;&nbsp; PS.to 0
&nbsp;&nbsp; rinseCS if cleanCS
&nbsp;&nbsp; yield if block_given?
&nbsp;end
end #samplePassF
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<property name="body"><![CDATA[Present:&nbsp; Bill, Elif, Chris P, Julie, Jim, Roman

h3. &nbsp;Items:


h4.


h3.


h4. &nbsp;1.&nbsp; JdF

* Ball had to be reopened to switch a communications pin.&nbsp; Will use this time to reload some testing pucks.&nbsp; Will not change PCR reagents.&nbsp; Will re-seal later today.&nbsp;
* Doug planning on test tank Weds.

h4. 2.&nbsp; Drifter

* Julie working on MFB 1.&nbsp; Her assays have been qualified on another MFB, so currently concentrating on being able to filter 2L, and what this does to the SPE efficiency, etc.&nbsp; Should be getting Hawaii water end of this week.&nbsp; Will test with that and higher-pressure pressure pots.&nbsp;

h4. 3.&nbsp; Roman concentrating on array needs.&nbsp; Will work with Julie and Chris P. for arrays for Hawaii and SC Wharf, respectively.&nbsp;

* ESP-Bruce recovered and will be shipped back to MBARI July 11.&nbsp;&nbsp;
* TTLab will start to get reorganized.&nbsp; Helpful in build of Betty and re-build of NEO.
* Chris P., will be needing help with the NEO conversion and will rely on Roman and Bill for the script re-do's she can't get to.

h4. 4.&nbsp; Elif has rec'd the SYBR assays, and will load on MFB 5 Friday or Monday with Preston help.&nbsp; She's trying to get assays ready for potentially a M0 deployemnt in Fall, although this has not been confirmed.


h4. 5.&nbsp; Bill testing MFB recovery of DNA with Qiagen wash buffer.&nbsp; Also has got MFB4 assembled from parts of others;&nbsp; still needs calibrating, both plumbing and heater module.
\\]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim B., Chris P, Roman M., Wayne R., Cheri E., Brent R., Julie R., Scott J.

Absent:&nbsp; Chris Scholin, Doug Pargett.

h2. &nbsp;Issues:

\\

1.&nbsp; NEO preparationsball screw has been replaced with new one.&nbsp; Reagents corrected.&nbsp; CTD compatibility to be dealt with on the deck by 'hot-swapping' with one that works on MOE.&nbsp; Pressure differential error:&nbsp; must be the sensor.&nbsp; The two have very different response slopes, so will replace with a new pressure gauge. Discussion ensued on what exactly the logs looked like.&nbsp; Brent to look at the first deployment log.&nbsp; {color:#ff0000}We must look at temperature effects on pressure gauges.{color}

\\
2.&nbsp; CTD's:&nbsp; One must be sent back to Seabird and therefore will be returned with the newer firmware.&nbsp; We must get Bob Herlein to do work.

3.&nbsp; Roman to disassemble and do forensics on Bruce and Mack.&nbsp; Start Monday.

4.&nbsp; Cheri to visit McLane May 17.

5.&nbsp; Methane Mound cruise is gelling.&nbsp;A.&nbsp; Load WF July 21; shove off July 22

B.&nbsp; begin return to Moss Landing July 27; arrive July 28
LOCATION:a.&nbsp; WF will be in Los Angles Harbor, Berth 262 near Wharf and Tuna: &nbsp;[WF location|http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&msid=111102629856882203099.000485df2087907222856&ll=33.768636,-118.459546&spn=0.650709,0.787582&z=11|WF in S. Cal for Methane Mound]

b.&nbsp; Discussion ensued; we will use Benthos modem.&nbsp; Deckbox should arrive late this week.

c.&nbsp; Will use large Niskine Rosette

d.&nbsp; Get methane mound temperature to run D-ESP van for check-out. ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Bill, Chris P, Elif, Roman, Doug, Chris S., Scott, Jim

h3. Items


h4. 2012 Plan

* Discussion/explanation of the 'funding-line' sheet (green sheet--> [tasks for 2012.pdf|^tasks for 2012.pdf|2012 tasks])
* Chris discussed his thoughts for 900913, that include particle collection, in situ incubations, processing our archival samples, and finishing papers.
** Other things to work on will be continued development of deep array, HAB work, and tech transfer.

h4. Tech Transfer/Spyglass Issues

* &nbsp;Melancon has been sending emails around asking for help out at Spyglass as he starts getting his new stable of machines from McLane.&nbsp; We can help when we have time, as part of our Tech Transfer agreement.&nbsp; if he starts to pay anyone for their services, this must be declared immediately, and great care taken to separate MBARI resources from this for-profit company.

h4. E/M Cable Cones

* &nbsp;We will get a cost-estimate for making 8.
* Question is whether we should look at redesign of strain relief, or strain-relief connection, or is there a better way of keeping strain-relief screwed on?

h4. JdF

* What acoustic modem deckbox will we use?&nbsp; Check with Hans and Alana
* Must clean/straighten up high-bay for Open House Saturday
* ISUS ]]></property>
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<property name="body"><![CDATA[h5. Goal

This meeting is to give an update and a walk through of the ESP GUI components, to get feedback and to put out a list of requests for things moving forward.

h5. Attendees

* Kevin Gomes
* Rich Schramm
* Brian Schlining

h5. Agenda

# Walk through of Planning/DM GUI
## [Deployment Diagram|ESPAPP:Design]
## [Starting the GUI|ESPAPP:2G ESP GUI Application]
## Setting preferences (Directory is local, repo is shared)
## Create new Instrument
## Create new deployment
## Show file pane, explain, then sync
## After sync, look at PCR files
## Parse log file
## Tabs
### ESP (dashboard connection)
### Planned
### Actual (show log file location with spanning lines)
### Images (show image, metadata, log entry)
### Samples (show log entry)
### Ancillary Data (Grab Gordon, CTD, ISUS, time window)
#### Zoom, print, save
### Files (open in browser, refresh, push to repo)
## Repository
# Walk through Dashboard
## Show work to date
### Use feedback (split and view)
## Talk about [Dashboard data protocol|ESPAPP:Real-Time ESP state update protocol framework]
# Walk through of Image Analysis
## Demo
## Show [wiki page|ESP Image Analysis Application] for use
## Matlab

h5. Open issues

# Plan/Data
## Need way to determine exactly which contextual sensors on on ESP (CTD, ISUS, etc.)
## Need something in the log file that indicates when a DWSM inhale is done
# Dashboard
## Need to get data/simulator to start driving dashboard for development
## How do we then take this protocol and persist for playback (i.e. log file entries?)
# Image Analysis
## Got what he needs to keep going.

h5. Suggestions

# PCR Plots need separate axes for Temp and diode data.
# After adding assay, planned table does not updage]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Chris P, Elif, Roman

h4. Items:

# Cold testing for WHOI deployment.
## Elif has compared old wash buffer with 'modified' wash (50% wash, 50% buffer E) (at 2 degrees, viscosity of wash \~10, modified wash \~3)
### blocking effciency on blank filter is similar
### signal with biomaterial similar (BAC arrays)
### moving to test HAB culture; if no difference, then moving to run HAB culture in cold.
### ESP-Bruce going into cold on Thursday.
# Array printing
## Roman planning a massive, 1-week printing run in early Feb.&nbsp; Will try and knock out all WHOI arrays.

3.  Discussion about using an unbuilt MFB for G3 development.&nbsp; Each missing some parts.&nbsp; Must talk to Chris P before building to know what needs to be done.
\\

Discussion of schedule, both for WHOI deployment and JdeFuca in July.
\\

h3. +Machine Plans:+

&nbsp;Gordon \-\- D-ESP

Betty \-\- still to be finished; plan is June/July

Moe \-\- Spring deployment at M0 and Drifter in Fall

Mack & NEO-\- Fall Biospace deployemtn

Bruce \-\- WHOI spring deployemtn
\\]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris S., Jim, Brent, Doug, Wayne, Scott, Cheri
Absent:&nbsp;&nbsp; Addie (maternity)

h3. Machine Builds

* &nbsp;Feb 23 Cheri finishes core builds and calibrations
* New battery connectors for surface-can lids have been ordered.

h3. MFB

* &nbsp;Cheri will ship 3 MFB kits to McLane tomorrow.&nbsp; Chris S. will cut PO to pay for assembly of 2 of them.&nbsp; Kits will not have instructions included.&nbsp; Tim can get copies of things when he's out next week for core assembly
* USCS people now finished with MFB01 and we can proceed with integration on MOE.&nbsp; Will do it the week of Feb 17; next week Scott will work on single connector, week after that Cheri can do mechanical merging.

h3. Software

* &nbsp;Ruby patch on all machines except MFB02, MFB03, Gordon, and Betty.
* Brent needs more cables:
** serial & debug cable (10-pin to DB9)
** PCR w/ level-shifter
** J-TAG cables
* Discussion about the need for more (newer?) laptops.&nbsp; Brent and Jim will talk to Todd.
* McLane needs one laptop that runs LINUS.&nbsp; (this typo purposely inserted to see who reads these notes).&nbsp; Again, will talk to Todd about getting a machine.
* Checksum difference--Wayne DID get correct bits eventually, so gave to DWSM and seems to be working.
* Wayne, Brent, Scott, Doug to meet at 10am tomorrow to discuss DWSM issues
* Wayne thinks 1 more day on dPress stuff and hardware and he'll be finished with DWSM hardware
* new Ethernet extenders shipped out today

h3. DWSM


h6. +Sphere+

* Sphere is approved to 4000m\!&nbsp; Hooray.
* MACK is designated core for Deep ESP tests.&nbsp; During June Flyer cruise, we will be using a new build (TBD).
* engineering will get&nbsp; MACK the week of Feb 23.
* Doug can fit any core into sphere, giving time to cold-test MACK
* Before that, GG will be cold tested in chamber to \-2C, then put syringes on Mack.
\\

h6. +Elevator+

* &nbsp;CRP may be moving up their foam delivery date to mid-March due to some prior order cancellations
* It will need machining; still to determine who will do that
* Modem;&nbsp; we only have USBL transducers on the ships, but not lots of track record with this modem for both communications and release.&nbsp; Brent will talk to Dale Graves about this to help us decide what to go with.
* Although it's a back-burner issue, Doug will check with Flyer winch specs to see if it would be possible to use Spectra line to help place the D-ESP.

*{+}DWSM{+}*
* &nbsp;SeaConn will deliver elevator cable MARCH 13
* for wet-mate connector, we will use FOCE spare ODI connector--terminate exactly same way as on FOCE.
* Question as to whether the SIM-Can will go with us on the Northern Expedition.
* One pump on DWSM seems bad; Doug looking into getting replacement
* Brent will start working on DWSM control next week, after latest firmware on all dwarves.

h3. Other Items:

* &nbsp;light puck testing not yet finished
* Teflon retainers & O-rings--Chris S. hasn't done anything yet
* Need to re-machine puck top to accept new o-ring arrangement to hold against scintered frit.&nbsp; Doug to talk to Mark B/Mike Parker about this.
* Van.&nbsp; Will meet with Chris to discuss $$ for this.&nbsp; Needs to go down to 2 degrees C.]]></property>
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<property name="body"><![CDATA[&nbsp;Present:&nbsp; Cheri, Wayne, Scott, Brent, Doug, Chris S, Jim, Gene


Absent: Kevin, Addie


h3. Machine Builds

* Scintered frits to arrive March 25.&nbsp; Chris S. says no problem as they will not be used in April 1 deployment.
* Cold-rated 25ml syringe leaks when at 4C.&nbsp; GG's DID work at 4C so we could try it.&nbsp; Scott playing phone-tag back and fort with company.
* New CPLD code has been loaded into MACK; it will get 'exercised' by engineering while we fiddle with the core...

h3. MFB

* MFB's rec'd at McLane.&nbsp; Ivory is checking them out.&nbsp; No word on build dates.
* LLNL contacted about their first delivery of modules (supposedly on the 20th).

h3. Drifter

* Decision is to use Freewave modems.&nbsp; Will use our current radio box, which also contains GPS
* Foam arrives 1st week of April.&nbsp; THEN we can start superstructure build.
* Cable drum is taking time to build.&nbsp; Will be ready late March/early April.
* Currently electronics are giving problems--fried UART?&nbsp; Gene to work with Wayne.&nbsp; He also needs ME Tech time.

h3. Software

* &nbsp;Brent still to get the PCR module version to LLNL.
* we now have 50GB on the ESPShare--should last 1 year.
* Bruce seems to be running fine as a local machine (since Monday)

h3. Deep ESP


h6. +Sphere+

* Paul C and Tom M are currently wiring sphere bottom

h6. +Elevator+

* elevator fits sphere
* feet still to be installed
* foam being added to top today/tomorrow
* drop weight assembly still to be designed and manufactured
* Acoustic acoutrements on elevator: We'll use a pinger (we'll borrow, unless we want a more powerful one than we can borrow; then we'll buy), and another for data-transfer and release.



*{+}DWSM{+}*
* Doug able to manually create 4500psi on repaired pump.&nbsp; It is now installed into DWSM
* hold-up on DWSM is wiring the switch assembly; Scott to get etechs on this
* Doug has lots of loose ends to finish
* dPress CPLD; faults because switches are not 'sticky'.&nbsp; Wayne thinks it's software and will fix today.&nbsp; There have been some mechanical problems getting the switches to switch.
* Ruby code for DWSM.&nbsp; Brent will write something that will perform the tests we want to perform for this first deployment.&nbsp; Doug and he will talk mon/tues; we'll have a group mtg Weds to discuss the finalized testing.

h3. GUI

* Comments from Kevin:
** Rich and I sat down at got back working on the ESP log changes.&nbsp; We checked out the most recent code and got everything building and are generating missions with the GUI and running them on Rich's machine (in simulation).&nbsp; We are now looking back at the previous code changes Rich made and migrating them to the new code base to meet our needs for log entries. Brian is working on ESP image analysis. He has been focusing on Fourier-Mellin Transform (essentially FFT cross-correlation in log-polar space) but is not convinced it will work for the spot images. He's implemented the polar and log-polar transforms for images though, which will be useful for other image-registration techniques.&nbsp; He is exploring another method that looks more promising now ...

h3. Deployment Issues

* &nbsp;April 1 Surface.&nbsp; Roman will test radio
* New batteries already installed for GPS.
* Monday mooring will be moved to high bay.&nbsp; Much discussion about checking the radio and radio-link to Abe's house.&nbsp; Brent and Scott have a plan that will minimize Brent's time yet test all systems before deployment.
* Brent fixed our shore station at Abe's house by replacing their power supply wall wart.
* For the engineering test dives for D-ESP, we need to set up target sites for all dives.&nbsp; First one (April 7) will be 800-900m near MARS.
* Chris Grech has some operational questions related to the northern expedition RE: getting equipment up there and what people will need.&nbsp; Clague responded and Chris S. will forward that response to the team for further comment.

h3. Other Items:

* &nbsp;Discussion about ethernet hub in van.&nbsp; Will probably mount a 5-port hub on the wall.&nbsp; Still being discussed.
* Wayne, Scott, Chris S gone next Tuesday for TWIC card #1 visit.
* Northern expedition will require us to truck up our van, loaded with all our stuff.&nbsp; Logistics for this should be contemplated.]]></property>
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<property name="body"><![CDATA[Present: Chris S., Elif, Bill, Chris P., Julie, Jim, Roman, Nilo

h3. &nbsp;Items:


h4.


h5. &nbsp;1.&nbsp; JdF

* Assays from weekend run look fine (post-can QC).&nbsp; Rbcl PCR still showing some positive, and arrays showing some (minor) positives, but background looks good.

* Spares:&nbsp; We will bring Betty in the plexi-box as a 'spare-parts tree'.&nbsp; While there may not be a total rebuild on the trip, she would provide parts for a quick DWSM repair early in the deployment if needed.
* CTD:&nbsp; getting serviced (new batteries) today.
* The only thing Science needs to pack are another filter rig and some carboys.&nbsp; Working that out with Doug on where those should go.

h5. 2.&nbsp; Drifter

* CS on Moe has been fixed.&nbsp; Roman is waiting on leaky waste until Julie goes on vacation (next week) before looking into that.
* Using 'Final Purge' after each WCR and 'MFB Final Purge' before PCR seems to remove enough contamination and saves waste space.
* McLane has a newly designed larger waste container.&nbsp; \**we should look into purchasing, esp. for use with D-ESP.
* Julie has filtered 2L and 4L of Hawaii water.&nbsp; Takes about&nbsp; 1hr and 2:15, respectively through a 0.22um filter.&nbsp; She will do a power calc by comparing Watts up before and after.
* Here P/P are working; no inhibition despite larger amounts of seawater
* Roman to check carousel that was remounted.
* Arrays:&nbsp; Julie will set-up the probes and Roman will print while Julie is away.&nbsp; Julie will also list pucks she needs so they can be cleaned and ready-to-go when she returns. &nbsp;

h5. 3.&nbsp;&nbsp; Budget stuff for 2012 proposal


* Chris P will get her 900913 template to Jim for this year's budget input.
* Bill U. presented addenda to the budget that we will incorporate into the proposal.
* Any big-ticket items we need:&nbsp; a milli-Q water system?

h3. &nbsp;Other Items:

* Roman heading to Spyglass this afternoon to help them with Lysis test---they need help.&nbsp; Their machine also seems to have a leak as bubbles are forming in one line.
* Does Spyglass machine have a name?
h5. Neo Rebuild
*** Seem to be having the static issue we've seen on other machines.&nbsp; Host needs a capacitor.&nbsp; Scott notified.
*** the new Ruby code does not work on NEO.&nbsp; This issue may need to wait until Brent gets back
h5. CTD Issues
* CTD used on Fall, 2010 cruise needs calibration (Fluorescence to Chlorophyll was off by factor of 3).&nbsp; Chris P, said adjustment was done on the fly by comparing CTD with actual niskine casts at 20m.
* There was also the CTD with the mis-calibrated chlorophyll; where is this CTD and what's been done?
* Bottom line:&nbsp; Roman will inventory the CTD stable.&nbsp; Find out what range Julie wants in Hawaii, and get one adjusted for that range.
h5. MFB Issues

* MFB 4 will be the lab 'drop-in replacement' machine
* We will build up one more from the parts of two (and it still needs major software upgrade) for lab testing.
* We need a sense of who is doing what with the MFB's.&nbsp; We want to make sure and accomodate:
*** Mark Strom at NOAA
*** Steve Hallum at UBC (Steve will be coming here for sabbatical during 2012 to learn how ESP works)]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Doug, Wayne, Cheri, Chris S., Scott, Kevin
Absent:&nbsp; Gene, Addie (maternity)

h3. Machine Builds

* Gordon and Betty.&nbsp; Cheri predicts 3 weeks to finish if hands don't give her too many problems
** Maxon stopped making old motors, and these new ones (with mylar cable) produce much less torque.&nbsp; Maybe windings are for higher voltage.&nbsp; Cheri will test.&nbsp; We currently have 1 old motor and 3 new ones.
** We ordered 2 more harmonic drives.&nbsp; Moe has GG's lower hand and it will need to be changed out

* HV pucks.&nbsp; Tops have been machined.&nbsp; Doug or machine shop can turn spacers.&nbsp; Cannot get different softness of o-rings from McMaster, although Chris doesn't think we need different ones.

h3. MFB


h3.

* 3 MFB's have been shipped to McLane for build.
* Spoke with LLNL yesterday.&nbsp; John promised 2 modules by March 20 (2009).&nbsp; Then 4 by end of April, then 4 remaining 'after' that.&nbsp; New modules have different firmware (v 4.04 vs 4.03), so we'll have to get our two switched eventually.&nbsp; New firmware expands the data buffer and has better error handling.

h3. Drifter

* Gene out today.&nbsp; Wayne will start communications testing next week.&nbsp; Not using TCP, so this might be a problem.&nbsp; Will go with freewave modems (not iridium) and GPS for the drifter deployments.

h3. Software

* &nbsp;Bruce has been running the new software off the network for several weeks with no problems.&nbsp; Monday Brent will burn this software into Bruce's flash, and we'll start exercising it as a local machine.
* Much discussion about Bufflehead being full and Chris P losing data.&nbsp; We need a science data-manager (John Ryan?).&nbsp; Currently need to delete old stuff.
* Today, Brent will backup and delete stuff older than 1 year.
* Jim will go to IS to see if we can get more space on the ESPshare, although cost may be prohibitive.

h3. Deep ESP


h6. +Sphere+

* Paul Coenen continues with wiring.
* Vicor mounting brackets are finished.&nbsp; Assembly continues

h6. +Elevator+

* elevator is back from LA, but there may be some distortion.&nbsp; Doug going out for a look this PM.
* We can finish elevator construction with Mike Conway and Paul Coenen.
* Scott will move foam and other crated sphere half out of parking lot and into bldg D.

*{+}DWSM{+}*
* Switch boards are finished and we'll give to Wayne after this meeting so he can test his dPress code.&nbsp; Then we can put bags in oil.
* High pressure pump.&nbsp; Still waiting for return from Emeryville.&nbsp; 4500psi will get us to 3000m.&nbsp; We have a fall-back site if we need to go to only 1800m.
** During the 'repair', some parts were re-machined, thus we hope that fixed things.&nbsp; We will tighten bolts on current pump we have hoping that will stop back-flow above 2000psi.
** If nothing works, our options are to go to shallower sites where not as much pressure is needed.

h3. GUI

* &nbsp;Brian has begun work on image analysis software.&nbsp; Working with Nilo.
* Rich coming back to project to work on parsing data files.

h3. Deployment Issues

* &nbsp;April 1-28 surface deployment using BRUCE.&nbsp; Roman will get divers and is leading this Zephyr deployment.&nbsp; Will use NEWEST mooring.&nbsp; Brent/Cheri will work on radio testing.&nbsp; Scott will get Jose's group to ohm-out E/M cable.
* April 7, 14, May 1 \-\- Deep ESP tests using MACK (with new low-temp syringe plungers).
* May 12-June 11 surface deployment using MOE w/PCR (if ready).

h4. {gliffy:name=table\|space=ESPAPP\|page=12Mar2009\|pageid=9372226\|align=left\|size=L}


h4. Crews

Zephyr surface:&nbsp; Chris S, Roman, Nilo, Cheri

June 5-9 Flyer:&nbsp; Chris S. Jim, Doug, Scott, Brent, Gene, Chris P., Roman, Julie, (Vrijenhoek), summer student

August 15-27 Flyer:&nbsp; Chris S., Doug, Scott, Brent, Chris P.
\\

h3. Other Items:

* &nbsp;Van is level and external power connections finished.&nbsp; Still must be wired internally.
* Chris S and Julie at CMORE in Hawaii next week; gone March 15-19.
* Jim will be gone at ASTID reviews March 30-April 3.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Bill, Elif, Chris P., Roman, Doug, Nilo, Chris S., Scott, Jim

h2. Items


h4. Jdf

* Instrument is ready to go.&nbsp; Wed will load water to do post-transport QC.
* Packing logistics:
** gas bottles are aboard
** ESP-Betty will be loaded on ship in plexibox
** Bill working on MSDS's for silicone oils, battery oil, batteries, He, and N2
** Truck arrives Wed at 9am for loading.&nbsp; Will be met in Newport by Chris P. on Friday morning.&nbsp; Bill/Scott/Doug arrive in Newport late Sunday night.
* Mission Plan
** The starting plan is [HERE|^JdF_TimeLine_06_27_11.pdf|Mission Plan] and Ruby script is [HERE|^JdF_mission.txt.pdf|Ruby script].&nbsp; Weather and any number of unforseen events may cause on-the-fly changing.&nbsp; Good Luck\!\!

h4. Proposal planning

* Will check with engineers regarding travel and capital purchase items next year

h4.  Other Items

* No Science or Engineering meeting next week.  We will have informal get-togethers before Friday.]]></property>
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<property name="body"><![CDATA[h3. Items:

1.&nbsp; Event Detection Discussion
* &nbsp;Issues with event-detection on surface moorings are very complicated due to types of fluid-flow near the surface

* Much discussion on whether nitrate would be a better trigger for upwelling than temperature.&nbsp; Chris P. was asked if she can provide old ISUS and array data to see correlations.&nbsp; Yes she can.
* We will develop this for a surface deployment; logic will be on the ESP but thresholds will be adjustable from shore.
* We could also run this in 'test' mode, where it notifies shore that it should do something, and waits for instructions from humans.
* ACTION:&nbsp; We'll see how the data look to gain confidence we can get it to fire at the correct time.&nbsp;

2.&nbsp; D-ESP
* D-ESP is now opened, unhooked from MARS simulator, and in the van.
* Need to know what housing we will deploy with the mass spec.&nbsp; Does it need different mounting brackes, etc.&nbsp; Bill to look into by contacting Peter.
* ISUS-\- the two deep ISUS housing have arrived.&nbsp; Doug will high-pressure test them the first 2 weeks of Feb.&nbsp; We still need to get the high-pressure probes ordered (Jim will ping Luke)
* Bill looked into turbidity issues at the 'Ashes' vent site.&nbsp; Unlikely we will need a 'prefilter' on the wand, but there may be issues with wand length.&nbsp; Must get requirements asap for any necessary development.
* Calendar is attached to last week's Engineering mtg notes.

3.&nbsp; Drifter comms
* Brent has looked into Iridium phones and believes a solution exists to use these on Drifter (and an other mooring that needs to go Iridium).
* We are moving forward on getting a loaner phone here to test before purchase.

4.&nbsp; Spyglass
* Although details are murky, Chris Melancon may have opportunity for contract work if anyone is interested.&nbsp; This would consist of being a tech-support 'lifeline' for newly sold ESP units.&nbsp; Please talk to Jim if you have any interest in this.

5.&nbsp; WHOI
* WHOI phone conference tomorrow at 11 to discuss EOM mooring design.&nbsp; We will have a preliminary mtg today at 2 to discuss the issues before tomorrow's phone call.
* &nbsp;When we ship our mooring to WHOI, we will be using old DSP&L (orange) battery boxes (with alkalines), not the new tubes we are developing.
\\]]></property>
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\\

&nbsp;1.&nbsp; MARS testing end date.&nbsp; Will unhook next Tuesday.&nbsp; We have not been able to make MARS gag again.&nbsp; Craig Dawe would like us to go completely to 375V, so we can go back on the same port.&nbsp; We may retain 48V so we can talk to it, should the 375V go down.
\\

2.&nbsp; About 1.5 weeks left to perform MARS clean-up.
\\

3.&nbsp; Shop has lost a person, and water jet is down, thus very busy.&nbsp; New CNC arriving in Feb.
\\

4.&nbsp; Reagents to be checked at Spyglass.&nbsp; The 0.1um filtered stuff has never been produced by them; we will probably send someone to oversee production.
\\

5.&nbsp; Much discussion about JdF calendar.&nbsp; [Here it is|^Calendar JdF 2011.pdf|JdF calendar].

6.&nbsp; G3 discussion.&nbsp; Scott brought test fixture to show off.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Elif, Roman, Nilo, Chris S., Jim

{color:#ff0000}Roman on vacation Aug 1-14.{color}

{color:#ff0000}Chris S on vacation Jul 13-19.{color}

h2. Items


h4. ESP-Bruce at WHOI

* &nbsp;We will have Bruce K. remove temp-sensitive reagents and FedEx to us, and we will ship equipment back in Unrefrigerated van ($5800 vs $9200).&nbsp; Because of Keafer's schedule, ESP will not be shipped until July 25.&nbsp; Roman sending Hobo temp sensor to see what temp swings the van experiences.
* We need to spot-check the ESP temp calibrations upon return, just to be sure.

h4. Pucks

* &nbsp;We have had 1200 puck pieces in need of serial number etching.&nbsp; We've rec'd the first 400 back from the etcher.&nbsp; Nilo is inspecting and will ready the next 800, probably in batches of 400.
* We've also rec'd pucks owed us from McLane (already serialized).&nbsp; These need to be inspected and Roman planning on doing lysis test with them.

h4. CTD

* &nbsp; Newly rebuilt fluorometer seems to give same readings as an old working model.&nbsp; Roman/Nilo doing an 'at-sea' test right now--I'm watching them out the window bounce around in the Whaler.
* We need to know the range the fluorometer needs for the clean water at Station Aloha.&nbsp; It may need 100x sensitivity.&nbsp; So, order of events:
*# Confirm {color:#0000cc}{*}CTD-4894{*}{color} is working
*# Call Kilo Muana for their CTD sensitivity settings
*# Call/send to Seabird to make the change
* Once drifter cruise is over, we will need to lower the gain for 'normal' use again.&nbsp; Next use may be the CA current drift in the Fall, 2011.

h4. Drifter Cruise

* We have the Shana Rae lined up for at-sea test either week of Aug8 or Aug15.
* Next Tuesday (Jul 19) we will meet with Julie & Roman to start _intense_ logistical planning.
* Chris would like to meet with Julie later in week to discuss:
*** All data collected so far on MFB related to drifter preparations
*** Progress on ISME paper
* Roman has array printing for this deployment completely under control.

h4. Sybr HAB Assay development

* &nbsp;at 400nm, results on ABI looked good.&nbsp; MFB look similar to AOAb.&nbsp; Raised primer concentration and got much better signal on MFB.
* Elif rec'd many cultures of various pseud's and is making plasmids, as these cultures have become difficult to get.

h4. SC Wharf Deployment


* We will start the ball rolling on this now.&nbsp; Looking at a mid/late October deployment.
* Should check with Ralphe about his CTD and the wharf guys about installing a new pump (Sept.)
* Elif would like to continue helping the QC of arrays, so it's not all up to one person (Chris P has Aug vacation, as does Kevan in Sept.)

h4. Other Items

* We will decide by July 22 whether we will participate in the CANON Sept cruise.&nbsp; Things to learn by then to help in decision:
*** what would be the mission?
*** Are we chasing upwellings or is it HAB related?
*** repeat of Spring deployment with adaptive sampling?&nbsp; Yanwu would need to be involved.&nbsp;
* We have new grant numbers for 2012
*** SURF Center \--&nbsp; 901205
*** Detection Chemistry \-\- 901204]]></property>
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<property name="body"><![CDATA[Short, touch-base meeting with Jim, Scott, Brent, Kevin, Wayne.

Main issues:\\

dPress code reveiw will be week after next.

Wayne still to port C-code from old tool-set to new tool-set.

Drifter to use Iridium modem.&nbsp; Does Brent know about this and is he good with it? ]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

|| Event || Example || Rule Used || Information Parsed ||
| Mission Start | {noformat}."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"{noformat} |{noformat}^GoodNews\\.\\S+\\s+\\\"Starting\\s+w/pucks\\s+in\\s+tube\\s+(\\d+).*Subject=>\\\"(\\S+)\\s+begun\\\".*{noformat} | # Starting tube
# Mission name |
| Ancillary Data | {noformat}#\Can@13:19:34, 48.2V, 17.3C, 44% humidity, 14.5psia, 14.84V, 0.42A, 0.413A avg, 6.21W
CTD@13:24:25, 3.3694C, 999.623 decibars, 3.1914 S/m, 104.61%, -0.180 1/m, 0.33 ml/l, 3.0760C
ISUS@13:24:45, 24.460 uM/L no^3, -1.000 uM/L hs, 22.7800psu{noformat} | # First it removes all newlines from the log entry and then checks to see if the entry may have ancillary data by using the pattern {noformat}^Can@.*{noformat}
# If it matches, then it takes the original log entry, splits it by newlines (I replace '\' with newlines earlier in the process) and then pattern match each line with {noformat}^(\\S+)@(\\d\\d):(\\d\\d):(\\d\\d),(.*)${noformat} to search for time, source and the payload of the message. | # Source
# Time
# Payload | 
| Process Run Start with Archive | {noformat}#pcr sampling at most 1000ml, wcr at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml, wcr at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume
# Archive Target Volume | 
| Process Run Start without Archive  | {noformat}#bac wcr sampling at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume | 
| Start Sample | {noformat}#t\Sampling 100.0ml{noformat} | {noformat}^Sampling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| Stop Sample | {noformat}#t\Sampled  100.0ml{noformat} | {noformat}^Sampled\\s+(\\d+\\.*\\d*)ml.*${noformat} | Actual Volume | 
| DWSM Start Sample | {noformat}#t\Sample Bag inhaling 5000.0ml{noformat} | {noformat}^Sample Bag inhaling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| DWSM Stop Sample | {noformat}#tWaiting up to 90s for Sample Bag to stabilize at 2279.4psia +/-25.0{noformat} | {noformat}^Waiting up to (\\d+)s for Sample Bag to stabilize.*${noformat} | Nothing | 
| Image Capture | {noformat}#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
\Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr11jul1500h2000ml40s.tif: TIFF Upload Complete{noformat} | Uses two patterns: 
# One
{noformat}^.*Exposing\\s+(\\d+)x(\\d+)\\s+pixel\\s+(\\d+)-bit\\s+image\\s+for\\s+(\\d+\\.*\\d*)\\s+seconds(.*.tif).*${noformat}
# Two 
{noformat}^(.*)\\/([a-zA-Z0-9]+)(\\d{2})([a-zA-Z]{3})(\\d{2})(\\d{2})h(\\d+)ml(\\d+)*s*\\.tif${noformat} | # One
## Image file name
# Two
## ProcessRun name
## Exposure Time | 
| Errors | {noformat}."Qmail"BadNews.suppressMail "Aborted by MAIN during Intake/Exhaust Pump move",:Subject=>"Thread::Aborted in readyDWSM"{noformat} | {noformat}BadNews.\\S+\\s+\"(.*)\",:Subject=>\"(.*)\"{noformat} | Error Message |

h3. Assumptions

# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.

h3. Graphical Form

The flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}
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<property name="body"><![CDATA[Present:&nbsp; Chris S., Jim, Kevin, Brent, Doug, Wayne, Scott
Absent:&nbsp;&nbsp; Addie (maternity), Cheri

h3.


h3. Machine Builds

* Weeks of Feb 8 and Feb 23 are on for the McLane core builds.&nbsp; Chris S. will confirm with Tim.

h3. MFB

* &nbsp;Cheri will be finished with core kitting by Friday.&nbsp; Then its on to MFB kitting.&nbsp; Goal is to send to McLane by Feb 8.&nbsp; McLane will do tubing cutting.&nbsp; We will update this schedule the 1st week of Feb.

h3. Software

* &nbsp;New Ruby patch (R7) has checked out on Moe.&nbsp; Next Thursday will install on Mack/Bruce/Neo.
* Brent's Ruby patches have been adopted by the gods of Ruby, the Japanese. (This is a big deal, that he should bring to his 2009 review\!)
* New puck handling code will be installed with the R7 patch.&nbsp; Now the hand will move a little closer to the pucks when positioned over the carousel to make sure the hand closes on the puck.
* Brent is modifying the log file formats so less CPU time is spent parsing the date /time stamps.&nbsp; He explains this [here|ESPAPP:Parsing the Raw ESP Log File Format].
* It was decided that Rich Schramm, working in the Ruby data-management end of things will create branches in CVS, checkout code and test and then merge back in.&nbsp; Kevin will direct this.
* Wayne has found Dwarf code problem.&nbsp; He's getting different checksum numbers, depending on his build platform.&nbsp; He and Brent will devise some tests to determine where problem lies.

h3. DWSM


h6. +Sphere+

* Doug has created PO for SWRI
* Will ask Cindy to organize trip to SWRI

h6. +Elevator+

* &nbsp;Mike P. still working on drawings, but unknown progress
* John Erickson still analyzing frame, but coming up with screwy numbers; model may be wrong.
* FOAM:&nbsp; Trellenberg being difficult and now saying delivery is March 30-April3.&nbsp; We have several workaround options:
** Mike Conway says they (DMO) have 12 ft^3 (or more) of 34lb foam we may be able to use
** This amount may only allow 4 batteries and maybe no CTD
** Could supplement with glass spheres, but there is a 6-8 wk lead and possible redesign of float housing to accommodate.
** DECISION:
*** Will use 'Mike" foam and supplement with FOCE foam or use some of Ken Smith's 40lb foam.
* Modem on elevator:&nbsp; nice to have so we can ping without having ROV to plug in.&nbsp; Deck boxes; who has them--we may need to purchase.

*{+}DWSM{+}*
* Have been running pumps and looks like we will be able to get 6000psi out of them.
* Intake exhaust is running--energy draw is within design limits
* CABLES--critical path issue.&nbsp; 8 week lead time from Seaconn;&nbsp; Scott trying to push them, especially on terminations, but they are rigid in time estimate.&nbsp; Unclear if the 8 weeks is with or without terminations.&nbsp; Will keep checking in with them.

h3.


h3. Other Items:

* &nbsp;For March and April sphere deployments, we will use MACK.&nbsp; In May will decide which core to mount with PCR.
* Chris thinking about purchase of 4000m Spectra line for better positioning of D-ESP during deployment.&nbsp; Question is whether winch on Flyer can handle the heave loads, yet to be calculated.
* We need both Teflon retainers and snap O-rings.&nbsp; Science wants the manufacture/drawing #'s for these.&nbsp; Will attend to when we all return.
* Chris has found the High Volume pucks.&nbsp; Doug has good idea for easy modification.&nbsp; When we return, will start process for ordering 20um, 10um, and 0.1um scintered frits.&nbsp; these will be tested in spring/summer surface deployments.
* We need new types of battery connectors on surface can lids.&nbsp; Scott to scope options.

Jim gone to ASLO tomorrow Jan-23 thru Feb 2.
Chris S., Chris P., Brent, Scott heading to LabAutomation in Palm Springs 1-23 thru Jan 28.

Chris S. leading meeting (gathering) next Thursday.]]></property>
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<property name="body"><![CDATA[Present: Jim, Wayne, Brent, Doug, Scott
Absent:&nbsp;  Chris S., Cheri, Addie (maternity)

h3.


h3. Machine Builds

* &nbsp;

h3. MFB

* &nbsp;

h3. Software

* &nbsp;Wayne can make the bits w/ his version 10.1 tools
* Brent mentioned syringe loses home position periodically, so Wayne will apply similar testing that he's done to rotary valves
* Next week will start work on dpress and ethernet extenders for Drifter
* Bufflehead is now on an UPS as is MFB01
* Brent has finished calibration code for R-valves
* Latest version of Ruby patch code is MBARI17.&nbsp; Will test on Moe.&nbsp; We are using Ruby 1.6.8 with this latest patch code (new Ruby is 1.8.7)

h3. DWSM


h6. +Sphere+

* &nbsp;Sphere passed vacuum leak testing
* Packed for SWRI and will be sent tomorrow (Friday)

h6. +Elevator+

* &nbsp;Mike P. working on drawings
* John Erickson doing some acceleration models of the structure
* Foam--Trellenberg (TX) is having manufacturing issues with 30lb foam.&nbsp; Doug looking into alternatives

*{+}DWSM{+}*
* Scott and Wayne have got software/electronics to the point of turning motors
* Mike P. handling small job issues
* Now are dicussing cable lengths for elevator
* We will use FOCE's connector cable, but final connector for MARS will be different.

h3. GUI Development

* &nbsp;

h3. Other Items:

* &nbsp;]]></property>
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<property name="body"><![CDATA[h3. Minutes
This was a meeting that the GUI team held to get back on track for development for 2009.
{section}
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h5. Status update
GUI is being used for planning and some data processing.  The log file parsing is creating all kinds of issues with application deployment due to the Ruby requirements.  Brent is OK with changing to log file to allow us to rip out the Ruby stuff which should fix deployment issues.
h5. Log file processing
Brent was OK with us putting in log entries however we wanted.  He will be tagging all log entries with an epoch seconds offset from a base timestamp further up the log file.  That should work OK because we can put fully atomic log entries in our entries. Rich will work on the ruby code and Kevin will work on the GUI to consume those.  Not sure how we will implement, integrate and test the changes.  Kevin will talk to Brent.

h5. Image analysis
Brian will be working on the ESP stuff in March and he wanted to make sure that it is known that he may only get to a point where he understands the problem based on the days he was given.  He currently has software that will find spots and calculate intensity.  He can find and label spots with intensity.

The issue is taking the report from the filter paper print job and align the image with that map.  Once this is done, the rest should move forward, but this alignment, scaling, rotation is the key issue.  There are products out there that do this type of analysis, but they are commercial and proprietary.

The goal of this work will be to have an image in the GUI with the spot map overlayed and a key that has the various spots and their labels with their intensity.  This could then all be saved off to a text file for analysis/import.

h5. Action items
# Kevin to talk to Brent about process for change and test
# Rich will work on ruby so that our log entries can be included
# Kevin will work with Rich on consuming those log entries in the GUI
# Starting in March, Brian will work on image software.
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* Kevin Gomes
* Brian Schlining
* Rich Schramm
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<property name="body"><![CDATA[h3. Science Meeting

Present: Jim B., Roman, Chris P., Chris S., Bill
Absent: Julie (deployment), John (sick)

{color:#3300ff}1. Updates:{color}\\
* {color:#3300ff}Brian Schlining and image analysis{color}
** Science has met with him to discuss/explain anomolies in the comp spot intensities.
** Chris S. states that the comp spots are not reliable indicators of background as they are very sensitive to small changes in what we a.)lay down on the membrane, or b.) signal probe concentration.&nbsp; This will need much work to fine tune.&nbsp; Meanwhile, Brian has enough to continue his image analysis work, which will pay dividends for the upcoming MRI.

* {color:#3300ff}John Ryan and his paper.{color}
** This was his email:
*** a) Paper
QC and analysis of 2008 environmental data (satellite, AUV, moorings) is done.&nbsp; This provided clear results relevant to explaining / supporting
the probe array signals, comparing 2007/2008, and highlighting observing system needs & challenges.&nbsp; I am culling the results pool and producing
final figures and an outline this week, to be circulated.
b) Drifting ESP
The trajectory data from last year's drifting ESP test has been requested from Gene.&nbsp; When I get it, I'll provide the data and a simple velocity analysis to the ESP team, AUV Ops & the Rajan lab.
** Chris S. mentioned that drifter position data was also located in the headers of the CTD casts, located here:&nbsp; \\Tornado\ESP\2009_ESP_Deployments\CTD data from WF cruise\sCTD Data Deep ESP jun 09

* {color:#3300ff}Array      printing update{color}
** Last Saturday we replaced Cavro pump.&nbsp; Nilo coming in this weekend to print arrays, but his schedule is becoming busier at school.&nbsp; Roman may have to step in and help.&nbsp; Two 'spare' printer kits have been ordered and delivered.&nbsp; We estimate a need of 70 HAB arrays, and 12 (Bac arrays?) for Gordon.

* {color:#3300ff}Bruce/Mack error analysis{color}
** Roman will put data in Jim's temp box.&nbsp; Looks like Bruce had one error, but Mack errored on each run.&nbsp; Jim will work up.

* {color:#3300ff}NEO deployment plan{color}
** Depoyment on May 20 will be Roman, Julie, and a TBD.
** Must replace ball screw that came undone; use a new one from Betty, not one from GG.
** Get Brent to look at pressure-out-of-range issue
** remove incorrect reagent
** CTD driver issue.&nbsp; Will talk to Brent about approaching Bob Herlien to write drivers for the newest Seabird CTD's.

* {color:#3300ff}Chris P. paper progress{color}
** Has been gathering papers for the abstract, introduction, and begun writing methods
** Will bring a package of figures next week
** looking at submission to PNAS or Applied Env. Micro.

* {color:#3300ff}Bill U.{color}
** Provided movie and some data on methane mound.&nbsp;
** 810m
** Lat=33.779, Long = \-118.747]]></property>
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<property name="body"><![CDATA[&nbsp;Present:&nbsp; Cheri, Wayne, Scott, Brent, Doug, Chris S, Jim, Gene

Absent: Kevin, Addie

h3. Machine Builds

* We will use GG syring in Mack.&nbsp; May only evacuate if DWSM does the pushes so should be okay.
* Gordon and Betty.&nbsp; Cheri originally send end of March for their completion, but schedule has slipped.
* Betty's elevator, syringe, and carousal are calibrated equal to Gordon.
* The new harmonic drives take 50% motor force to just get going (old took 20-30%).&nbsp; New mount is good, but this drive has more stiction.&nbsp;
* Brent mentioned that there's a stiction parametr that's changeable
* We will try stiction parameters at different voltages.&nbsp; Maybe try different motor manufacturers.&nbsp; Get more Maxon's?

h3. MFB

Our third module should arrive Monday, March 30.from LLNL.&nbsp; Notes related to it are [here|ESPAPP:Notes from delivery of 3rd module (April 1, 2009)].


h3. Drifter

* UART fixed.
* Foam arrives 1st week of April.&nbsp; THEN we can start superstructure build.
* Cable drum is still behind schedule.
* Everything bolted and both motors turning (level-winder and cable drum)
* Plenty of little things to do
* May 14 looking tight; waiting on core and gearhead for levelwind.&nbsp; If these don't come, we'll test with the temp core and rope
* Gene must get Freewave.&nbsp; Gene will give his RS232 and antenna needs to Scott.

h3. Software

* &nbsp;Brent still to get the PCR module version to LLNL.
* we now have 50GB on the ESPShare--should last 1 year.
* Bruce seems to be running fine as a local machine (since Monday)

h3. Deep ESP


h6. +Sphere+

* wiring is complete

h6. +Elevator+

* we will use Rover drop weight
* elevator feet still to be mounted
* Mike Conway says they have a pinger for us and manual release.

*{+}DWSM{+}*
* wiring is finished.
* Brent worried about I2C length

h3. GUI


h3. Deployment Issues

* &nbsp;2 bugs found in Bruce before it's surface deployment.&nbsp; Brent thinks fixes are straightforward & working with Roman on it.&nbsp;
* Looks like HAB antibody has ahd something pushed into it (maybe ruined).

h3. Other Items:

* Acoustic modem needs:&nbsp; Reset capability & external power& drop weight.&nbsp; Brent will check on modem voltage range.&nbsp; Brent & Doug will confer about this.]]></property>
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<property name="body"><![CDATA[Jim,

In addition to Dean's comments about unpacking the module (Before you power the unit up, remove the main cover, and remove the packing that holds the boards in place for shipping.):

The module in standby should draw about 160 mA at 12 V dc.

TEMP? should return about 690 (ADC values) at room temperature. You can also check FAN ON, FAN OFF, etc.

When you power up, use CALTEMP 0.0,0.036,0.0 to get the calibration in the ballpark before you do any Centigrade commands. The default in the current firmware is not right. You have to do this every time it is powered up.

PIDTEMP 50.0,0.1,0.0,300,500,100 seems to work well. The default in the current firmware is not right. You have to do this every time it is powered up.

For PCR with FAM, start with 100 milliseconds on Channel 1. For PCR with TAMRA, start with 400 milliseconds on Channel 2. The TAMRA is kind of noisy. For our PCR verifications, FAM at 100 ms started at 1500 and went up to 2500, and TAMRA at 400 ms started at 1000 and went up to 2070.

I don't know how much optimization testing you folks have been doing, but I found it was helpful in dye tests to run a routine with multiple integrations at each cycle. This could probably be used for PCR too:

0:TEMP,93,135000;1:TEMP,60,30000;2:READ,20,20,20,20;2:READ,100,100,100,100;3:READ,200,200,200,200;4:READ,400,400,400,400;5:READ,800,800,800,800;6:TEMP,72,15000;7:TEMP,94,15000;8:LOOP,1,45;9:TEMP,40,10000;11:ENDP?

There is a minor possibility of photobleaching with extra light exposure, but we have not characterized that.

John Dz]]></property>
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<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically (colors are same deployment)+

{color:#ff00ff}April 6--Bruce at M0 for surface deployment (Zephyr){color}

April 15--Mack in Sphere (dive #1) for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in Sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

{color:#ff00ff}April 29--Recover Bruce at M0 (Zephyr){color}

May 1--Mack in Sphere (dive #3) connected to DWSM; incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

{color:#0033cc}May 14--Deploy NEO w/PCR, surface deployment (Zephyr){color}

May 27--First Drifter dive; used weighted cable (Zephyr)

June 5-9 \-\- Western Flyer Trip.&nbsp; D-ESP, Drifter, and CTD casts. {color:#cc0000}{*}MOVIES{*}{color}:  D-ESP launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/DESP%20deployment%20(full%20quality).dv].  Drifter launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/Drifter.dv].

{color:#0033cc}June 11 \-\- Recover NEO.&nbsp; (Zephyr){color}\\

+FALL Network Deployment+

Proposed locations are here: [http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&msid=113879459163411006053.000471828af997bd7d89c&t=h&z=12]

{color:#ff6600}September 24 \-\- Deploy Moe w/PCR at M0.&nbsp; Deployed Mack at Santa Cruz{color}.&nbsp; {color:#66cc00}Deployed Bruce in the bight.&nbsp; (Zephyr)&nbsp; Lost communications with Bruce that day.{color}

{color:#66cc00}September 28 \-\- Recover (dead) Bruce.&nbsp; Comms box had water in it, but radio worked.&nbsp; EM cable had 2 broken wires. (Zephyr){color}

{color:#cc0000}September 30 \-\- Deploy D-ESP on MARS (Lobos).{color}&nbsp; Hand issue at first, but 'fixed' itself.&nbsp; Worked until Oct. 7 when wrong puck was loaded and water introduced into core, frying puck heater.&nbsp; We turned off and first recovery day (Oct 13) is weathered out.&nbsp; It still awaits recovery.

{color:#66cc00}October 14 \-\- Re-deploy Bruce (Zephyr).&nbsp; New comms box, re-terminated EM cable.&nbsp; Working well after deployment.{color}

October 20 \-\- Install pump system on pier at Santa Cruz Wharf. October 22 \-\- Neo installed on SC Wharf.

{color:#cc0000}October 30 \-\- Recover D-ESP off MARS (Lobos).{color}

{color:#ff6600}October 29 \-\- Recover both Moe from M0 and Mack from Santa Cruz (Zephyr).{color}

{color:#66cc00}November 2 \-\- Recover Bruce from the bight (Zephyr).&nbsp; This ends Fall Network Deployment.{color}

November 25 \-\- Recover NEO from SC Wharf.

{color:#ff00ff}December 14 \-\- Deploy D-ESP (Gordon) on MARS (Lobos). DWSM hiccuped on morning of Dec 28.&nbsp; 'Empty' switch seems damaged.&nbsp; Decided to stop sampling, exercise MFB with elution water negatives, and recover D-ESP on Jan. 7, 2010 w/ Lobos.{color} &nbsp;]]></property>
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# [Module 07 checkout notes (May 22, 2009)|^pcrmodule_checkout_20090522.xls]
# [LLNL-Spyglass meeting 29Oct2009]]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both CentOS.

h3. Prerequisites

# Clean install of CentOS 6.6 (this has gcc 4.4 by default)

h3. Steps to build and run

# I first logged in as kgomes
# Then opened a terminal window
# I changed to root using
{code}
su
{code}
# I then created the log directory by doing
{code}
cd /var/log
mkdir kgomes
chown kgomes:kgomes kgomes
{code}
# I made sure git was installed.  It was not so I installed it using
{code}
yum install git
{code}
# I also had to install autoconf using
{code}
yum install autoconf
{code}
# And I had to install yacc using
{code}
yum install byacc
{code}
# Then I changed to the root home directory using
{code}
cd
{code}
# I created a directory I could work in using
{code}
mkdir esp
{code}
# Changed into that directory using
{code}
cd esp
{code}
# I needed to build the MBARI version of Ruby, so I checked it out from Brent's repo using
{code}
git clone https://github.com/brentr/matzruby.git
{code}
# That created a matzruby directory which I then changed into using
{code}
cd matzruby
{code}
# Not sure why, but running ./espconfig did not work due to some path problems so to fix this, I edited the espconfig file and adding './' in front of 'configure' in two places
# Then I was able to run espconfig this way
{code}
./espconfig
{code}
# Once that completed, I ran
{code}
./espinstall
{code}
which installed the ruby executable in /opt/mbari/bin
# I then exited out of the root shell
{code}
exit
{code}
which put me back in my kgomes account
# I created a working directory by using
{code}
mkdir esp
{code}
# Changed into it using
{code}
cd esp
{code}
# I tried to clone the repository, but kept getting a 403 (unauthorized) error which I am sure had something to do with my git configuration as it would not ask for my username and password event though this is a private rep.  To get around this, I just opened a browser, logged into to github and downloaded the zip file which I put in the esp directory. NOTE: I did verify this works with the Git clone as well.  I had to create an SSH key and add that up on GitHub from the CentOS machine, then the git clone worked fine.
# Now, in order to setup the ESP environment so it can run on my machine, I edited my .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/esp/ESP2Gscript-master
export ESPname=gordon
export ESPmode=simreal
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin:/opt/mbari/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# Once this was done, I was successfully able to run
{code}
esp
{code}
to get the ESP server running]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# [Extracting the intensities values from the filter image (_Data Extraction_)|#data]

See also: [Applying Fiducial Marks|#fiducials]

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[Investigations into Automated Image Analysis^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}

h1. {anchor:data}Data Extraction

Without being able to align the filter image with the GAL points, it's impossible to:
# Associate a spot with it's content
# Accurately and reliable extract all spots of interest.

Here's a few examples of just trying to extract spots from an image:
{info:title=The Good}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_3-40s.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1.tif.png!
{info}
{info:title=The Bad}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-40s.tif.png!
{info}
{info:title=The Ugly}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}

h1. Summary

The only hurdle that needs to be overcome at this point is [pattern matching/image registration|#matching]

Here are the signficant hurdles for _pattern matching/image regsitration_:
# Reliably extracting spots from the filter image
#* In my test images, I was only able to extract all spots in one image using thresholding techniques.
#* Another technique to try would be edge detection. This may be problematic in noisier images though. 
# Dealing with symmetry in the spot layout, this confounds most image registration techniques.
#* It would be great if I could get some *key spots* that I can reliably detect and differentiate from the other spots. For example, 2 spots that are near the edge of the disk. If I could extract those then, I would be able to easily register the GAL file with the image. As an example, look at the image above an notice the single spot near the edge of the disk. If we had 2 of those on that image it would make my life much simpler!! ;-) ALthough in order to use those I would need be able to extract the same 2 spots from the GAL file.


h1. Applying Fiducial Marks for Image Analysis

If the ESP arrays had distinct fiducial marks it should be possible to locate these marks and use them for scaling and rotation of the GAL to match the array image. Ideally these fiducial's should be either the closest points to the center of mass of the or the farthest points from the center of mass.

h2. {anchor:fiducials}Applying Fiducials. 
* During analysis we extract the spots that are visible using a thresholding technique. This give an image like this: 
!fitler_3_aoi_masked.png!
* From this mask we can calculate a center of mass of the image. (The blue dot represents the center of mass) 
!filter_3-center-of-mass.png!
* To easily locate fiducial it would be best if they were either the points nearest the center-of-mass or farthest from it. The red dots in the images below represent notional fiducial points.
** Example of points nearest COM: 
!filter_3_center_fiducial.png!
** Example of points farthest from COM: 
!filter_3-distal_fiducial.png!




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<property name="title"><![CDATA[2016 Deployments]]></property>
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<property name="body"><![CDATA[# [4K Sphere]\\

h2. IEMI number for Sable 5000:


h1. 300034012099780

{color:#006600}The Sable is the emergency locator beacon that starts transmitting GPS coordinates{color}
{color:#006600}once instrument package surfaces.{color}
# [Sable 5000 Iridium Beacon Manual v. 2.0|^Xeos_Sable_manual.pdf|v2.0]
# [Sable 5000 Iridium Beacon Manual v. 2.1|^Xeos_Sable_Manual_2.1.pdf|v2.1]]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]
# [04Sep2008]
# [11Sep2008]
# [18Sep2008]
# [25Sep2008]
# [02Oct2008] (Pre-deployment discussions)
# [09Oct2008] (the day after deployment....)
# [16Oct2008]
# [23Oct2008]
# [30Oct2008]
# [06Nov2008]
# [13Nov2008]
# [20Nov2008] (Scott's in charge)
# 27Nov2008 (no mtg--Thanksgiving)
# [04Dec2008]
# [11Dec2008]
# [18Dec2008] (Brent's in charge)
# 25Dec2008 (no mtg--Christmas)]]></property>
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<property name="body"><![CDATA[h3. Functional Requirements Document for D-ESP Wand

*Rev. 1.1*

*Feb 14, 2011*
\\

1.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand shall be capable of collecting a DWSM water sample and providing contextual sensor water from a point (ROV positioned) up to 10m away from the D-ESP and at a two position height; in the vent between \-30 to \-20 cm, above the vent, 20 to 30 cm above the seafloor. ROV may be used to switch positions.

2.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand shall operated at water temperatures up to 120°C. \[_121 °C is considered to be the temperature limit to life_\].

3.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand shall also be capable of collecting a DWSM sample and providing contextual sensor water from a point nearby the ESP, at an ROV positional height between 100 and 150 cm above the seafloor.

4.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand shall measure water temperature at the collection point (measurement signal routed possibly thru the CTD). Minimum temperature accuracy is ±1 °C and resolution is better than ±1 °C. Measurements shall be collected at 15 second intervals during inhalation and at 2 minute intervals all other times. Minimum calibrated temperature shall be 0 °C. Maximum calibrated temperature shall be approximately 150 °C. Measurements shall be available real-time to be displayed in the control room when the ROV is connected to the D-ESP via cable, and recorded within D-ESP for post-deployment analysis.

5.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand shall prevent particles greater than 0.5 mm in the longest dimension from entering the collection tube for DWSM. No particle exclusion is required for the contextual sensor water.

6.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand shall include sufficient cooling capacity to deliver water that does not exceed 25 °C to DWSM, the contextual sensors, and water pump.

7.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand shall deliver water to the contextual sensors at a constant flow rate (±??) between 500 and 1000 mL/min.

8.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;DWSM intake max rate shall be ½ of the wand delivery rate.

9.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand shall be flushed between sampling events so that uncontaminated water is collected and delivered to DWSM and the contextual sensors during subsequent sampling events. It would be preferable that the contextual sensors do not make measurements of contaminated water at any time and that continuous time-series are collected throughout the deployment.

10.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand and tubing shall be managed and protected, during deployment and recovery, to prevent damage and fouling with ROV hydraulic lines, manipulators, and/or the thrusters.]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 3, 2008*

*10:30am-12*
Present:  Jim, Cheri, Addie, Brent, Doug, Scott

h3. *Tech Transfer*

•&nbsp;&nbsp; &nbsp;Cheri; plan for hand cold-testing/re-valving by Jan 15

Bruce in chamber on Monday and running a shuffle (looped).&nbsp; It had stopped with forearm errors.&nbsp; Brent will help find when/why crashed.&nbsp; Restarted shuffle on Weds, but after awhile if gets worse and worse and stops.&nbsp; Does it both in cold and at room temp.&nbsp;

{color:#ff0000}ACTION:{color} Brent will show Cheri and Addie how to read log ({color:#0000ff}Brent & Cheri & Addie{color})

•&nbsp;&nbsp; &nbsp;Status of slow-running intake on GG

GG's pressure sensor broken.&nbsp; Found that the clamp holes were too small, and installation torqued the sensors so they were wrongly calibrated. Our fix is was to recalibrate when clamps are pressurized, but this masked the&nbsp; real problem.&nbsp; Not that pressure sensor mounting holes are correct, must run a sample on GG to see if it's smilar to NEO.

{color:#ff0000}ACTION:{color}&nbsp; run a sample on GG to compare to NEO ({color:#3300ff}Scott{color})

•&nbsp;&nbsp; &nbsp;Status of manipulator hands

Have one hand but lots of calibration issues.&nbsp; Parts for other two hands still on hold until first one works.&nbsp; Mike currently working on valve motor mounts and gears.&nbsp;

{color:#ff0000}ACTION{color}:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly ({color:#0000ff}Scott{color})

Will get one hand working then build 3 more.&nbsp; Cheri discussed the design of the linkage which make the hands not move together when they close.&nbsp; Currently all arms are the same (non-ideal) design.

{color:#ff0000}ACTION{color}:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands ({color:#0000ff}Doug{color})&nbsp;

•&nbsp;&nbsp; &nbsp;Drill out pressure sensor holes in clamps

{color:#ff0000}ACTION{color}: Will do this when we revalve the cores. ({color:#0000ff}Scott/Cheri{color})

•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?
sent an email but nothing back from company...
{color:#ff0000}ACTION{color}: call and find out where the company is in development ({color:#0000ff}Scott{color})

•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?
Jose adding up inventory.&nbsp; We will need enough for 2 cores and 8 MFBs and spares (at least 1 full core and enough spares for 8 MFB's\[3 dwarves, 2 R's\]).&nbsp; Tally up, look at production run, and scale up for best economy.&nbsp; Will place order early January.

{color:#ff0000}ACTION{color}: check with Jose and&nbsp; Tom ({color:#0000ff}Scott{color})

*•&nbsp;&nbsp; &nbsp;CMORE workshop Jan. 14-17*;&nbsp;
* roll-up core and MFB to Pacific Forum

* clean B125 lab
* clean up MFB (get rid of sleepy/medusa of wires/tubes, have a 'show' script)

Will take sleepy off MFB and give to Brent and substitute with dwarf, and Addie will work on cleaning and gussing up MFB

h4. Final Tech Transfer Issues

The plastic chamber box; should be as near the volume of the cylinder as possible.&nbsp; Will not be using endcap since it doesn't fit.&nbsp; Talk to Jim S. to build the&nbsp; box.

Connectors; have researched how to populate the lid--only one power, ethernet, console, contextual sensors (3), modem, external sampler.&nbsp; Will remove these from the 1K housing.

{color:#ff0000}ACTION{color}:&nbsp; move connectors from 1K to the test box ({color:#0000ff}Doug & Cher{color}i)
\\

h3. *MFB*

* Update on solid Phase Extraction.&nbsp; Protocol development?

SPE working well now.&nbsp; Further protocol refinements will&nbsp; wait until Chris P. has submitted her paper.&nbsp;
* place order with MAXON for MFB spares (Addie)

Ordered.&nbsp; just need the PO approved.&nbsp; 6-8 week lead time.&nbsp;
* Update on PSV valve addition and connection w/ core
* &nbsp;Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addie will figure out how to connect ports 3, 5, 6 with no bubbles. (Addie).&nbsp; They have been called; waiting for response.

•&nbsp;&nbsp; &nbsp;Report on syringe lubrication.&nbsp; Success?

Has lubed it several times, but still getting trajectory errors.&nbsp; The motor is at the edge of it's capability (moving almost TOO slowly).&nbsp; Addie has 2-3 motors with bigger gear box, 2-3 with better encoder, and 2-3 with both.

{color:#ff0000}ACTION{color}:&nbsp; will try many of these motors, then work on flipping. Must get to the slow speed of 1ul/sec. ({color:#0000ff}Addie{color})&nbsp;

{color:#ff0000}ACTION{color}:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this ({color:#0000ff}Scott/Brent/Addie{color})

There was discussion of running our reagents out at LLNL to see if we can emulate their results, but with our reagents.&nbsp; Will discuss with LLNL.

{color:#ff0000}ACTION{color}:&nbsp; talk to Tony and get timeline on next MFB ({color:#0000ff}Jim{color})&nbsp;

h3. *Software*

•&nbsp;&nbsp; &nbsp;Status of current Ruby version.&nbsp; Close to lock-down?

Brent has written a fix that is more efficient when bouncing between threads.&nbsp; So no garbage collection issues now.&nbsp; Was unable to recreate the error with DWSM, but found a problem with driving the I2C bus with a fast laptop--maybe something related to how quickly data is driven to the serial command bus.&nbsp;&nbsp;

Ruby interpreter is stable for this year.&nbsp; As close to 'frozen' that we'll get.&nbsp;

{color:#ff0000}ACTION{color}: Set-up sleepy board and an elmo on desk to emulate ({color:#0000ff}Brent{color})

{color:#ff0000}ACTION{color}:&nbsp; change laptops and ARM boards and install the new Ruby interpreter ({color:#0000ff}Brent{color})

{color:#ff0000}ACTION{color}:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] ({color:#0000ff}Brent{color})

{color:#ff0000}ACTION{color}:&nbsp; Work with the auto-cal code ({color:#0000ff}Brent{color})

•&nbsp;&nbsp; &nbsp;Issues for Wayne:
o&nbsp;&nbsp; &nbsp;Low power CPU replacement
o&nbsp;&nbsp; &nbsp;USB camera porting from Kernel 2.4 to Kernel 2.6
o&nbsp;&nbsp; &nbsp;Improve dwarve DC servo control algorithm
o&nbsp;&nbsp; &nbsp;Improve ESP hardware simulator (Ruby)

Low power CPU being put off until after spring deployment.&nbsp;&nbsp; Sirus (sp?) chip may work,&nbsp; but Russian company has a great sleep state DRAM board.&nbsp; From now to March, we should explore both these options.&nbsp; March we make a decision, and then bring in Wayne the help with the implementation.

{color:#ff0000}ACTION{color}:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; ({color:#0000ff}Jim{color})&nbsp;

h3. *Sphere and 4K DWSMS*

•&nbsp;&nbsp; &nbsp;New order of Pucks placed?&nbsp; Charges went through Chris S?
•&nbsp;&nbsp; &nbsp;Serial numbering of pucks
{color:#ff0000}ACTION{color}: Collect and inventory all pucks ({color:#3300ff}Chris S to get Nilo{color}).&nbsp; Then will send 1/2 to Mike Parker to be etched ({color:#0000ff}Scott{color}).&nbsp; Still be to done.
•&nbsp;&nbsp; &nbsp;Pressure pots.&nbsp; Ordered 1 five, 1 ten.

•&nbsp;&nbsp;&nbsp; Battery/power issues for spring deployments
stick with alkaline.&nbsp; Do we need more boxes?&nbsp; Need 4 boxes initially.&nbsp; Not working on low power issues.&nbsp; Must order minimum of 1 box of batteries in early 2008.

We need a total of 6 boxes for the spring deployment, and have 5.&nbsp; 4 of those 5 are D-cells.&nbsp; Two boxes will run around $4K (without batteries)

{color:#ff0000}ACTION{color}: &nbsp; Buy two boxes, populate with D-cells.&nbsp; One with lead-acid will remain lead-acid. ({color:#0000ff}Scott) Jim{color} get account # to charge.

•&nbsp;&nbsp; &nbsp;4K DWSM update
o&nbsp;&nbsp; &nbsp;machining
o&nbsp;&nbsp; &nbsp;proof of concept steel housing?
•&nbsp;&nbsp; &nbsp;Progress on 1K article?

Will not use Ti for the sampling system.&nbsp; Until we prove the aqualung works, no need to make out of Ti.&nbsp; So will make out of SS for around $8K for the housings.&nbsp; Next month we'll build up a plastic system we can run up to 100psi.

{color:#ff0000}ACTION{color}: will try and have model done by end of Jan--depends on pumps ({color:#0000ff}Doug{color})&nbsp;
\\

h3. *Items Pending:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)
Three new surface cans for 2008

{color:#ff0000}ACTION{color}: Get quote from Gene and place order ({color:#0000ff}Jim{color})

*Timeline (This schedule is its own page in Confluence):*
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Chris S., Chris P., Brent, Bill, Doug, Roman, Scott, Elif

h3. Jdf

1.&nbsp; Much discussion of wand and development necessary to implement the 'trident' structure, with temperature probes at each intake.Conclusions:

Mechanically, building a 3-intake system is similar in difficulty to a 2-intake system.

Temperature probe design will require new development.&nbsp; 3 probes will need data-logger, with associated wiring/cabling and pass through's.

Given the time constraints on engineering, we will develop a 2-intake system with only 2 temperature sensors; one at vent, one at elevator.&nbsp; Bill and Scott will look into temperature probes that will not require separate data logger and subsequent software development.&nbsp; Roman suggested Seabird's mini-CTD's and will ask them if they have probes that would work for us.
2.&nbsp; We will not be implementing the wiring necessary for an ion-pump in the ISMS for JdF.&nbsp; This development may occur for MARS in Nov, 2011.

These conclusions need to be conveyed to Pete.

3.&nbsp; Chris S. and Chris P discussed the need to develop a skeleton mission in order to start determining the pump 'calls'.&nbsp; They wrote a straw man on the board (Bill has copy of).&nbsp; As this matures we will fold into the overall JdF concept of operations.

h3. Other:

1.&nbsp; Potential site-visit to ASU in April.&nbsp; Dates still TBD.

2.&nbsp; We will plan a PDR for G3 in Nov, 2011. ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Birch, Scholin, Preston, Jensen, Pargett, Roman, Demir, Ussler , Massion

h3. Items:


h4. 1.&nbsp; Drifter discussion

* Iridium Radio Checkout
** Brent has rec'd loaner phone.&nbsp; Will activate today or early next week in order to test.
** Should be returned by end of next week, unless it works for us, then we purchase ($1200/ea).&nbsp; We need 2.
** We must purchase month-to-month&nbsp; b/c prepay doesn't support short burst messaging.&nbsp; Will test open connection and SBM.
* Data logger/Controller
** We must come up with functional req's.&nbsp; Gene will set up a mtg next week with the players:&nbsp; Gene/Brent/Scott/Chris P./Hans T.
* Wave analysis is currently being performed.&nbsp; Nov waves look like they get bad very quickly.

h4. 2.&nbsp; Spring Deployment

* For adaptive sampling, we need to use nitrate and salinity.&nbsp; May add temperature but much more variable than the first two.&nbsp; Chris P. to get this data to Brent.

h4. 3.&nbsp; WHOI deployment

* &nbsp;Brent testing his comms idea and works well in lab on >200' CAT5 cable
** BUT, outside it did not.&nbsp; signal only went 50' on CAT6; 100' or more on CAT5 it did not work.
** Possible issue was radio; must retry with another radio.&nbsp; If these adapters don't work, there are more expensive German ones that will.
* Bruce Cold Testing
** Elbow motor was maxed out (300cts/tick) at room temp, but at cold it could never get this high (e.g., 10C was 210cts/tick at 100 mA; at 2.5C was \~100cts/tick)
** Doug/Scott learned at ALA there are two types of harmonic drive grease.&nbsp; Unknown which we have.&nbsp; We should order new harmonic drive with low temp grease.
** Could also put spot heater on harmonic drive to keep it warm(er).
** Fingers on Bruce need tightening
** Should siliconize top and bottom of pucks to keep from sticking.&nbsp; This is an important CONOP to share with Bruce @ WHOI.
** currently running a cold spiked seawater sample to see effects on array.
* Need to start planning the forward team visit for radio testing, and MBARI's deployment
* Also, MRI team should go to exercise the software interface.&nbsp; Will speak with Kevin
* Must decide who will have access to instrumentation in the event of a crash.

h4. 4.&nbsp; JdF

* Girguis here Monday; have not heard from Vic about an ASTEP II phone conference update.&nbsp; Chris S. will try contacting her.
* Gordon Plans
** Scott will mount the modified combiner box (2 48V buses)
** We will pull Gordon out next week.&nbsp; Probably needs a once-over.&nbsp; Replace it with laptop 'brain' so Doug can continue testing DWSM.
** HP interface needs to come up to 4500psi, so modifications needed on various parts
** Testing of HP interface slated for week of Feb 14.
* Wand
** Doug's option; put pumps at ends w/ checkvalves.&nbsp; He's found some pumps that would work.
** We will test effect of the pump in-line with the sample
** must get an idea of the impact of flow-rte on ISMS--will talk to Pete next week
** pump will be closer to elevator
** 35C is max temp DWSM can handle.]]></property>
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<property name="body"><![CDATA[h4. First 'Tactical' ESP Science Users meeting

\\

Issues:

Roman
1. Comp spots still causing problems on array printing.&nbsp; Roman working on it and slowing his pace to interleave working on the instruments.
2. MOE is halfway apart/ Bruce is out of incubator.&nbsp; Both being worked on.&nbsp; Getting ready to test Bruce with chilled seawater sample.
3. Must start thinking of shipping to WHOI. New battery tube containers will not be ready. Using orange boxes.

Bill

1. Learning how to run the MFB.
2. He has his five-year review on Thursday.

Elif

1. Been helping out with QCing Roman's arrays. &nbsp;
2. Comparing new signal and capture probes
3. Building to cold-testing of cultures in cold seawater.

Chris P.

1. Data summary for MARS 2011 deployment is on ESPshare.
2. CTD and ISUS data for 2009 deployments has been given to Brent.
3. Pete has provided sequences and Chris may order tomorrow.
4. Presenting to Chavez group on Thursday RE: drifter and CANON cruise.
5.IPC--not needed for JdF. Should get it by mid-April with final batch by mid-May.&nbsp; No response from our explanation for sharing IPC outside MBARI. ]]></property>
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<property name="body"><![CDATA[h2.


h2. Scott Creek eDNA

{color:#ff00ff}March 25, 2019{color} \--&nbsp; Deploy ESP-Waldo at Scott creek with 132 archival pucks.&nbsp; Initially will sample 3 times/day (6am 12pm 6pm), but that will change.&nbsp; Powered by Jensen's homegrown solar array.

{color:#ff00ff}May 6, 2019{color} \-\- Recover ESP-Waldo, and replace with ESP-Moe.


h2. \\

\\]]></property>
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<property name="body"><![CDATA[h1. Cartridge part numbering

\\

Numbering convention of cartridges from May, 2018 is [here|^Cartridge Numbering (24 May 2018).xlsx|3G cartridge numbering].]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 8 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|https://drive.google.com/file/d/0B8RHIr7J8XHoclQ3d0pUMU5Ua2c/view?usp=sharing] to your computer.
# Double-click the jar to run the app.

You can also get the automated image analysis application [here|http://www.mbari.org/staff/brian/software/esp-automated-imaging-0.3.jar]

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|Investigations into Automated Image Analysis].

I'm working on a new method. Documentation is [here|ESP Automated Image Analysis 2]

h1. How to use it


h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls

!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.
{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size.
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result

!filter_3-20090430221134.png!

h3. Data Result

{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
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<property name="body"><![CDATA[h2. ESP Image Analysis Application
There is a standalone user interface for the ESP lab to run automated image analysis at [http://www.mbari.org/staff/brian/pub/esp-autoanalyzer.jar].

h2. Overview of ESP Image Analysis Automation

# [Investigations into Automated Image Analysis]
# [Extracting GAL Point Features]
# [Extracting Image Point Features]
# [Extracting Image Fiducial Features]
# [Point Feature Alignment]

h2. Source code

The source is hosted on at [https://bitbucket.org/mbari/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]]]></property>
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<property name="body"><![CDATA[h2. Overview

In order to automate the image processing, we need to know the layout of the spots as they were defined in the original GAL file. The instructions below illustrate the steps needed to extract this information.

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!ESP Automated Image Analysis 4^110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!ESP Automated Image Analysis 4^110220hab5wcomp_2011-03-07_150545_Run-single.png!]]></property>
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<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. The basic algorithm works as follows:

h1. The Alignment Algorithm

h2. The Basics

The basic building block of algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

Why use a chromosome to represent the points? Originally, feature alignement was done using a genetic algorithm, but it's been refined so that we now use some considerable less complex. 

The goal of our feature alignment is to find a non-rigid transform that rotates, scales and translates the gal points in euclidean space to align with point features extracted from the image. The recipe for this has several steps:
# [Read the GAL file and extract points for a single filter|Extracting GAL Point Features]
# Extract the fiducial points from the single fitler's gal points.
# [Read an ESP image and extract the bright fiducial spots|Extracting Image Fiducial Features]
# [Read an ESP image and extract all spot features|Extracting Image Point Features].
# Run through all the possible permutations of aligning the gal points to the image fiducial points
## Calculate the fitness for each permutation
## Select the _fittest_ alignment.

The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [linear transform|https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala] needed to rotate, scale, and align the GAL to the image and apply this to all the points in the GAL file.
# Calculate a fitness for the match between the image and GAL points. This fitness is actually a mutlipart evalucation
## First check that all the transformed GAL points are within the bounds of the image. If they are not we evaluate this match as _unfit_.
## Second, we check that the GAL points have not collapsed by calculating the most common distance between nearest neighbors. Then we check to see that this distance less than the maximum distance between image point pairs and greater then the minimum distance between point pairs.
## Finally, we use a weighted distance function. This calculates 
### the distance between all image points and all gal points. 
### Selects the GAL point nearest each image point.
### Takes the _distance_ parameter (we're using 7 pixels) and if the GAL-Image point distance is less than our distance param, we use the following {noformat}f  = fitness
d  = maximum distance [provided by user]
n  = number of image points
dn = distance from image point to nearest GAL point{noformat}
!fitnessfn.gif!]]></property>
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<property name="body"><![CDATA[h2. Extracting _Spots_ from ESP Images

The spots extracted from the image are used to calculate the fitness of the match between the GAL file and image file. 

h1. The Short Version
The first step is to read the raw tiff image:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = io.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}
!Extracting Image Fiducial Features^pcr11jun2520h2000ml40s.png!

There is a small function call that extracts the image spots. 
{code}
import org.mbari.esp.ia.imglib.MultiPassRegionsExtractorFn
val regions = MultiPassRegionsExtractorFn(image)
val points = regions.map(_.centroid).toSeq
{code}
The above code snippet does the following:
# Extracts the bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{regions.map(_.centroid).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of points is then converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(image).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val circles = points.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
io.write(colorImage, new File("pcr11jun2520h2000ml40ss-with-extracted-spots.png"))
g2.dispose()
{code}
!pcr11jun2520h2000ml40ss-with-extracted-spots.png!

h1. Under the Hood

In order to extract the regions that represent the spots we threshold at multiple levels using 2 different image treatments. The 2 image treatments are:
# Raw (no treatment)
# Standard deviation of image using a local 3x3 kernel.

We calculate a base threshold for each treatment using _maximum entropy_. Then we make multiple passes across the image from using the following:
{code}
val bound = 25 // Add and subtract this from threshold to get range
val minVal = if (split - bound < 0) split else split - bound
val maxVal = if (split + bound > 255) split else split + bound
for (i <-  minVal to maxVal by 5) {
    // Process image. ie. apply threshold and floodfill
}
{code}

For each pass across an image, we aggregate all the regions into a collection. During the aggregations we eliminate spurious or duplicate regions by:
# Exclude non-round regions. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest (e.g. {{filter(_.eccentricity()._1 < 3)}})
# Exclude regions that contain less than 10 pixels. 
# Exclude regions whose centroid duplicates an existing accepted region. (i.e. {{c1.x == c2.x && c1.y == c2.y}})
# Drop regions whose centroid is within 3 pixels of another region. These are likely to be regions that represent the same spot.


[Extracting Image Point Features 2]]]></property>
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<property name="body"><![CDATA[h3. Minutes from ESP GUI Demo and Question and Answer Session

The purpose of this meeting is to show the progress to date on the ESP Data Management/Planning GUI and to use this demonstration to foster information gathering that can be used to both direct development and answer development questions.
{section}
{column:width=60%}
This is the list of all possible consumable resources:
# Instruments:
## Darlene
## GIGI
## NEO
# Lists of phases, protocols
## HAB
### SH1
### lyfil
### SH2
### WCR
## DA
### DA1
### Dalyfil
### DA2
## BAC
### SH1
### lyfil
### SH2
### WCR
## invert
### SH1
### lyfil
### SH2
### WCR
## BACAR
### WCR
## QC
### WCR
# Details for phases:
## Max duration
# Details for protocols:
## Duration
## Delay to sample
# Consumable Types:
## Fix
## AgMeOH
## ab1
## ab2
## Lysis
## Dilutent
## Sig1
## Sig2
## Sig3
## Con 1:5000
## Sub 1
## Sub 2
## Wash
## CSR Flush
## CSV Flush
## PSR Flush
## Kill
## Waste
## Power
# Bags/Containers/Storage:
## How big are the capacities for the above consumables?
# Protocol Makeup
## For each of the phase/protocol combination, what consumables to they use and how much (i.e. recipes)
{column}
{column:width=40%}
{panel:title=Agenda}
# Introduction/Recap
# Demonstrate GUI to date
## How to start it.  Click here: [http://predator.shore.mbari.org/esp_gui/launch.jnlp]
## Should work on Java 1.5+
## Right now you will need to be connected to MBARI intranet (that will change to local laptop installation)
## Upper left is list of instruments and their associated deployment.  Default start is to have all displayed.
### Display selection tree functionality
## Year selection drives the overview calendar displayed below.
## The overview calendar always shows all deployments
## Click on overview calendar to select month of interest.
### This drives main calendar.
{panel}
{panel:title=Questions to Answer}
For GUI:
# Default is to have no deployments displayed.  Is that OK, or should have they all show up to begin with?
# Should I show all deployments on the overview calendar?
# Should consumables be decreasing meters and turn red on low?
# How much detail (zoom) do you want to see?
# Where do you want to edit phases/deployment (table/popup/etc.)?
For Mission Scripts:
# What is 'startTube' and how is it determined?
# What are the 'rules' around script construction? 
{panel}
{column}
{section}
{panel:title=New Requests From Meeting}
# Link the colors of the instruments to the deployments
# Have the deployments disappear on the overall calendar as well as the main calendar
# Clean up the view on the overview calendar so they don't look so busy (remove protocols and phases)
# Darlene is no longer with us, just GG (or GiGi) and Neo.  But there should be three new instruments coming on line.
# In the details pane, there was a desire to put the sample volume right next to the protocol name.
# When you select a protocol line in the details pane, a tab should be available to show the contextual data (CTD, ISUS) for the time span of when the sample volume was drawn
# There was a desire to have the CTD data displayed like the tide data is displayed and some way to turn on/off view of it
# Look into the possibility of using jruby to generate the mission script so the generation could be done outside of the planning application and changed there instead of inside the planning app.
## As a side note, you need to know the start tube in order to generate the mission script and the start tube will not be known till after the instrument is loaded.  Question, can't we tell the user how to best load the instrument based on the deployment configuration?
# There was a bit of discussion on the consumables view and how to use it in the planning phase.  I think the following was the resulting desire:
## When creating a new plan (deployment), the consumables should simply show how much of each consumable is being predicted (ml, watts, waste generation)
## Then at some point, the instrument will be 'loaded' and the view should be changed/enable that shows the amount of consumables are available (maybe also show how much is predicted to be consumed).  A full load will show all progress bars as 100% (display will show appropriate units like ml or watts) and then the bars will decrease as the log file is read and the actual amounts consumed are known.
## There was also a desire to know how many of the different phases could be configured with the current state of the instrument.  This speaks to the 'interrupted deployment scenario' where the instrument would be recovered and could be reconfigured (but no consumables added).  For example, if the instrument was recovered and it was half way through its consumption, the user could ask the application how many of the different phases could be run.  This would entail changing the pucks around, but the consumables would be left alone.  There was some talk about that just simply constituting a new 'deployment' since a new mission script would be created anyway.
{panel}




h5. Comments

[~brian] We have the database modeled to support ESP from planning through analysis. My take though is that we should create discrete applications for the different phases of the ESP deployment lifecycle (Plan, manage, analyze). There are a lot of _like to have_ features so we should manage the user expectations and tell them what is possible to do in the short amount of time that we have.. We're currently focusing on the planning/script generation phase, which I think is appropriate. Everything else should be deferred until we get a solid planning app put together....just my 2 cents.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Bill, Doug, Roman, Scott, Kevin, Jose
Absent: Scholin, Preston, Elif

h3. &nbsp;WHOI Deployment Issues

&nbsp;1.&nbsp; Discussion with Bruce K. this morning.&nbsp; He's reserved R/V Connecticut, April 17-23.&nbsp; Also has the R/V Tioga on hold.&nbsp; * Don Peters @ EOM has finished mooring design and lowered pump power req's through the gumby hose by lowering flow rate.
* They are shooting for a mid-March assembly date.
* They are ready to order Freewave modems and Brent will re-send them his suggestions.
2.&nbsp; Must talk to Theresa to begin the shipping issue.&nbsp; We will be sending ESP-Bruce, a surface mooring, and many spares (bugees, etc.)

3.&nbsp; Discussion ensued about a 'travel pack' that would allow shipment of ESP and surface mooring anywhere in the world.&nbsp; One big-ticket item is He Leak Detector; do we need a 'to-go' one?&nbsp; Consensus is we should have a leak detector; risk too high to not check.&nbsp; Doug had looked into leak detector options 1-1.5yrs ago.&nbsp; He will dig up old research.&nbsp; Perhaps we can purchase a hand-held that is better than our current one, but not as massive as the Pfeiffer.

4.&nbsp; Jose attended to get clarity on battery priorities: This was result
|| machine || Deep-ESP \\ || Bruce || MOE || ROV-Sledf ||
| Currently | 4 Lead Acid in O.Boxes \\ | &nbsp; (6 alkaline O.Boxes \\ | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ) | nothing |
| We need \\ | 8 lead acid O. Boxes \\ | 2 alkaline O. boxes \\ | 2 alkaline air-packs \\ | 8 lead-acid gels \\ |
| when? | June | April 6 \\ | April 7 \\ | June? |
129 Alkaline packs ordered (10 batteries/pack).&nbsp; Each deployment (Bruce, Moe spring, Moe Fall) will use 40 packs.

5.&nbsp; Brent has been in contact with Ivory RE: comms on the WHOI gumby.&nbsp; Ivory got 9600 baud using RS 422, but needed a ground, which was unusual.&nbsp; To make the WHOI comms work Brent estimates a week (5 full days) of work, which seems reasonable given our S. Cal experience.

6.&nbsp; Bruce is being reassembled and should be in the cold by Friday PM.

7.&nbsp; Will hold a 'travel' meeting tomorrow with Brent, Roman, and Kevin to hash out logistics of their travel to WHOI.&nbsp; Jim's office @ 11am.

h3. Jdf

1.&nbsp; Temperature probe is achilles heel.&nbsp; We've decided to go with RTD detector, and working with Scott has come up with the following design:
\\

{gliffy:name=probe\|space=ESPAPP\|page=Feb 17\|pageid=15990837\|align=left\|size=L}

2.&nbsp; must check that CTD does switch this channel off when CTD not running.

3.&nbsp; Scott to create a parts list for this design

4.&nbsp; Bill to order variety of sheaths and RTD sensors

h4. 5.&nbsp; DWSM

# &nbsp;Gordon now out of ball
# HP interface\--new pump is in-\-system will need a full flush
# Torque wrench found for pulling bells together for HP testing.&nbsp; Procedure is worked out.
# ISUS cans have been pressure tested and passed.&nbsp; To be handed off to Luke after they drip dry.
# New ISUS cable has arrived.
# Pulse dampers are in shop.&nbsp; Should be finished mid next week.
5.&nbsp; Travel issues:\* Van gets dropped in Newport on Friday.&nbsp; We'll run the dock QC Saturday and Sunday.&nbsp; Would be easier to leave van on trailer with generator.
h3. Other:

1. Shop is slammed.&nbsp; Know this when submitting stuff.]]></property>
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<property name="body"><![CDATA[h4. ESP Science Users meeting

Issues:

h5. Chris P.

# (some) probes ordered for JdF.&nbsp; Some were too clipped in the melt-curve analysis and we're waiting for new sequence from Harvard&nbsp;
# Gordon out of Ball but still with some reagents.&nbsp; Chris to run some samples collected at diffuse vent field at JdF in 2004 to see if we can get both PCR and SHA from same sample.
# Working on PCR paper.

h5. Bill

# JdF wand design
## Spoken with Geoff Wheat who suggests getting into the vent crack.&nbsp; deeper into crack = higher temperature = more microbes. Geoff has two Antara temp probes he might loan.&nbsp; Also could get some custom HOBO's, but these wouldn't be real-time.&nbsp; Scott being consulted....
## Roman waiting to hear from Vince @ Seabird.&nbsp; They are suggesting some options, but unclear whether their temperature gauges can go hot enough.&nbsp; Currently choices are A.) Seabird, B.) interface our own probe, C.)Adam Schultz--contractor who might make us probes.&nbsp; Will work with engineering on making this decision.
## Some discussion of alternative site with hotter vents.&nbsp; Currently think that will have max of 40C at Ashes vents.
## There will be no sediment at ashes.&nbsp; It's&nbsp; ROCK.

h5. Elif

# Ran experiment looking at array sensitivity of array when lysed from pressure pots vs. on bench.&nbsp; Both results were similar.&nbsp; This is bedrock work before going into cold temperature.&nbsp; Ultimately trying to see if cold reduces our array sensitivity; does a correction factor need to be introduced based on environmental temperature.

h5. &nbsp;Roman

# &nbsp; Bruce being reassembled and will perform the room temp tests (full run) end of this week.&nbsp; Then into cold over weekend, and cold test early next week.
# Clamps on MOE would not compress the o-ring, so poor thermal contact on both clamps with pucks.&nbsp; Mike P looked at and found that grooves were too shallow.&nbsp; He will examine drawings and fix.&nbsp; Jim will email this issue to McLane.&nbsp;

h4. &nbsp;OTHER ISSUES:

&nbsp;Chris S. sent email to Bruce K asking what their decision was for this spring deployment.&nbsp; Still waiting to hear.

Optode:&nbsp; Two types: Clark is sensitive to oxygen, but also to H2S and needs frequent servicing.&nbsp; Optode needs far less servicing, but is less sensitive at low oxygen concentrations.&nbsp; Should we get Seabird to add an optode to one of our CTD's?&nbsp; Decision was yes, we could use both types.&nbsp; Will charge to 900915. ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Cheri, Wayne, Scott, Brent, Doug, Chris S, Jim, Gene

Absent:&nbsp; Scott, Addie

h3. Machine Builds

* Rec'd 50um frits from Chand Eisenmann and it looks like they tested the thickness to our old (thinner) dimensions. &nbsp; Chris S. will take and check with Roman to see if we need to return.
* The new harmonic drive on Gordon is working very well.&nbsp;
** &nbsp;Today Cheri will move fluids then
** 2 days of temperature calibrations then
** science testing
* Two additional harmonic drives to arrive end of April.&nbsp; These for Betty and Moe (where we'll replace the hybrid GG hand)

h3. MFB

* We currently have 3 modules from LLNL:
* &nbsp;#1 is on NEO.&nbsp; #3 is on Moe.&nbsp; Just Received #4.&nbsp; All are running firmware version 4.03
* Much worry about how tightly heater boards are being held-should check before putting in water to make sure they haven't shaken free.

h3. Drifter

* Many COTS parts arriving.&nbsp; Lebus Core should be in this week.&nbsp; Surlyn buoy in.&nbsp; level wind motor shipped on April 9.&nbsp; Level wind gearhead shipping April 17.
* No core will be used in any May cruise.
* Will be using stitch-weld can with soft line
* Gene needs Scott/Brent help with network configuration to route packets correctly.&nbsp; We should start testing on desktop ASAP in order to be ready to use this on June cruise.
* Will try and move May 18 day to later in the week so not so close to May 14 cruise.

h3. Software

* Wayne to laod new bits for CPLD into DWSM this afternoon.
* We will modify the ethernet driver in the Linux kernel and put on {color:#cc3366}GORDON{color} to get it tested before Axial.&nbsp; {color:#ff0000}This will occur the week of April 27{color}.
* Brent ordered wireless dongles; we want to speak to the core with no cables--set to occur for the June Flyer cruise.

h3. Deep ESP


h6.

* Doug thinks elevator may be light, thus the mis-match with how many blocks of foam we needed.
* 4' sling was best lift length for ship's crew
* O-Ring pinch.&nbsp; In future will use star-pattern of tightening.&nbsp; Ideas for 3rd, gas compression groove discussed.
* Brent getting DWSM set up for development work with Scott on Friday.

h3. GUI

* work continues.&nbsp; After June cruise and NOAA visit, will go to a new log file format.&nbsp; So currently we will exercise new log code in {color:#cc3300}Gordon{color}.

h3. Deployment Issues

* &nbsp;For April 23 deployment, plan is to close sphere Tuesday, April 21 at 2pm.&nbsp; This may slip but must be started Weds morning.&nbsp; Science will have all reagents loaded by Monday AM for the next two dives.

h3. Other Items:

* Still to be done:&nbsp; Acoustic modem needs:&nbsp; Reset capability & external power& drop weight.&nbsp; Brent will check on modem voltage range.&nbsp; Brent & Doug will confer about this.]]></property>
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*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

*Dec 2, 2013*\--Fired off final sample.&nbsp; Recover slated for Dec 11, 2013. Ran a total of 24 samples, each with an archive.

*Dec 11, 2013*\--Successful recovery.&nbsp; Sable never fired, and significant corrosion around ISMS intake, but overall looks very clean. (later learned old firmware in Sable never turned off GPS; batteries dead upon recovery; as of Jan 22, 2014, Xeos was sending USB dongle to reprogram the firmware...)


h4. {color:#ff00cc}Puget Sound{color}

_{+}Lummi Bay:+_

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)

*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.&nbsp; Subsequent investigation found that modem card had been cancelled with T-Mobile due to NOAA miscommunication.&nbsp; When new one was tried, operator did not know to 'close the door' on the modem in order to power the card.&nbsp; Brent flew up and fixed.&nbsp; Missed 4 days of sampling.

*August 18*\--Lummi Bay deployment ended.&nbsp; Machine returned to NOAA.

_{+}Samish Bay:&nbsp;+_

*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; No CTD.&nbsp; Both machines have MFB and PCR.&nbsp; Media event was July 18.

Aug 14--Recover Gordon

Aug 17--Deploy (swap) NEO.

Sep 10--processing syringe servo motor has failed.&nbsp; Decision to run out remaining mission with archive only.

*Sep 16*\--NEO's mission ends.&nbsp; NOAA to recover and Roman/Kevan retrieved both machines Sep 25.

h4. {color:#ff00cc}ECOHAB/CANON--Monterey Bay{color}

*&nbsp;September 10, 2013*\-\- Deploy 2 ESP's in Monterey Bay.&nbsp; First time in southern part of bay.
\\

{color:#cc3366}*'North'*{color}
ESP-Mack.&nbsp; Lat 36.9048, Long \-121.93659, Water depth 32m, Can depth 9.8m.

*Oct 11, 2013*\--Battery voltage dropped too low, and we had to end mission

{color:#cc3366}*'South'*{color}
ESP-Bruce. Lat 36.63908, Long \-121.87884, Water depth 60m, Can depth 4.8m

*Oct 10, 2013*\-Found 'terminal fluid retention' on processing side-pulled an oring or some type of leak. Tried porting waste to Waste2 (known to be empty), but same results.  Final 3 samples to try and collect for SEM work.
\\

*October 21, 2013* \-\- Recovered both instruments]]></property>
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<property name="body"><![CDATA[h2. Methane cruise
\\

1.&nbsp; The team has performed an amazing job dealing with issues as they arise, and the sphere is closed, tested, and almost ready to go.&nbsp; Some issues about the heater in the ball, and how it has not ever been calibrated, but we believe it will be plenty warm enough, especially when plugged into the ROV.

2.&nbsp; The final science test in Gordon will be July 15, a core negative which will finish on July 16.

3.&nbsp; Elevator has been Test Tank tested and needs ISMS/CTD testing once more (tomorrow).&nbsp; Zincs to be put on ISMS housing.&nbsp; Acoustic modem needs new batteries.

4.&nbsp; Mike Conway working on placing tie-downs in the van.&nbsp; Flat-bed arrives/load/leaves MBARI July 19, and will get to LA harbor around midnight.&nbsp; Generator to power van arrived yesterday; Scott working with Day electric to get correct connector.&nbsp; Unknown how long fuel tank will power generator (trucking company does not know).

{color:#3300ff}KUDOS to Doug and Scott for handling the lion's share of D-ESP preparation for travel.{color}

h2. M0 Flip

1.&nbsp; We will be deploying NEO on August 3, recovery TBD, possibly with Shana Rae.&nbsp; Roman will lead this deployment, remaining crew TBD.

h2. Drifter

1. &nbsp; Gene has 3 drifter days planned:&nbsp; July 12, July 23, August 6.&nbsp; The first will be using empty, good (not stitch-weld) can.&nbsp; Second and third deployments will have MACK and each will probably run one complete phase.&nbsp; MACK currently needs some hand adjustments to ready it for a massive Tina McKlusky workout August 9-16.&nbsp; Roman will be working on this with Cheri.
\\

h2. &nbsp;Visitors:

1.&nbsp; Vanessa (?) from U. Georgia.&nbsp; August 1-31, then returning for BIOSPACE, Sept 28.&nbsp; She will be optimizing PCR assays.

2.&nbsp; Liz Ottesen.&nbsp; Here now, working to optimize (decrease) the amount of time needed to fix samples, once collected.

3.&nbsp; Tina McKluskey from Doucette Lab.&nbsp; She will be creating standard curves for DA on Bruce & Mack, Aug 9-16, in preparation for BIOSPACE.

I think the above are correct.&nbsp; apologies for mis-statements or misspellings.
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<property name="body"><![CDATA[Present:&nbsp; Wayne, Jim, Doug, Brent

Absent: Cheri, Scott, Kevin, Chris S.
\\

h3. Machine Builds

* Betty cold testing--3 issues:
*# at 2C there are borderline issues with carousel viscous friction, most definitely at \-5C.&nbsp; Inn current firmware, we can just run slower so no overcurrent.&nbsp; In new firmware we can limit PWM so there is no overcurrent (it'll just run at different speeds at diff temps)
*# Elbow misses and retrys--does it at 2C and more often at \-5C
*# Hand won't close around clamped puck--this was the Mack issue that we've been unable to repeat.&nbsp; Has Cheri looked at hand alignment?

Brent will check with Julie to see when MOE will be cold-tested.&nbsp; Still working on getting a new box from Scholfield built.

h2.


h3.


h3. MFB

* heaters #10 adnd #12 arrived today

h3. Drifter&nbsp;


h3. Software

* Brent working to merge our 3 firmware versions.  All looks good but he's now wrestling with code to allow different acceleration/deceleration rates.
* Brent would like to collaborate with UCSC people for radio comms for the fall triple-deployment.

h3. Deep ESP/DWSM

* PISSer
** Doug and Brent discussed many details of Pisser architecture
** Will move GG on Monday; plug in when Scott here and re-create problems seen on Flyer cruise
* Pressure Transducer 
** Will go with Stellar in NJ.  Will go with 8-pin out; Brent waiting for final quote.  Will approve PO today.

h3. GUI


h3. Deployment Issues


h3. &nbsp;Other Items

* discussion of G3 ESP showed that we need a better list of functional requirements for this next generation ESP.  What does science want to accomplish with this new instrument, where must it work, for how long, what are weight/vol constraints, etc.  We will start thinking of something to go in the LRAUV, but these questions need answering before serious engineering can occur on mechanisms...]]></property>
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<property name="body"><![CDATA[I started a bigger refactoring of the code because our assumption of ProtocolRun to samples were a little off.  The first assumption was that only ProtocolRuns had samples and they were a one-to-one relationship.  When we implemented this, we basically just put sample attributes on the ProtocolRun class.  With the addition of the MFB, it was clear that that is no longer the case.  With the ESP, a large sample is acquired from the ocean and then several steps can be taken on that sample.  So, knowing that, it made more sense to abstract out ProtocolRun to just a ProcessRun and then create a Sample class that could have Samples as children.  This was done so that you could define a Sample and then split that sample into children that could be processed in different ways.  This better matches the way the ESP actually operates.  I am also taking this opportunity to move us back to MSSQL so that the production database is truly production.  In order to do this, I took these steps:

# Created a DTS job to read data from an ODBC connection to the MySQL database and populate the correct data in the MSSQL database on fog.
# Created a new class called Sample.
]]></property>
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<property name="body"><![CDATA[ESP team, please add to the questions:
* What will be the typical length of deployment for the Gen 3 instrument (G3)?
* What is the overall energy budget?
* Do we need our own power source or use the AUV?
* What size will the G3 be designed for?&nbsp; LRAUV size, El Dorado size, or something else?&nbsp;
* Maximum Depth
* Maximum Sampling Depth?

* What is the main function of the G3 instrument?&nbsp; Front end water processing, creating a lysate for back-end analysis?&nbsp; Or will the G3 do more than that? What?
* If simply water processing:
** how much water will be filtered?
** What will be the filtering system?&nbsp; pucks? modified pucks?&nbsp; scintered frits? something else?
** what lysate volume do you want to create?
** Will archival be necessary?

* If G3 runs assays, how many assays/tests will it be running?&nbsp; Frequency?
* Reusable assay's?
* How will decon occur?

LRAUV Payload Specs:
* 300m design depth
* Typical payload size: \~11.5" dia, 12" long
* Maximum payload size \~11.5" dia, 24" long
* Must be neutrally bouyant
* Must include presure housings and buoyancy (if needed)
* AUV power may be used, with reduced range/duration.

Software questions:
* What will be the information (commands) required from the AUV?  For example, will the samples be fired by geolocation, by data from ancillary sensors, by time, etc.? Depending on how the ESP is to conduct it's mission, it may need changes to AUV payload (contextual sensors, specific commands where the AUV can tell the ESP to fire, etc.).]]></property>
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<property name="body"><![CDATA[This page documents some of the HMI/SCADA packages that are available for Java that we might use to build the instrument state GUI.  Here is a table documenting the aspects of the various frameworks:

||Framework||Company||Description||URL||Cost||Licensing||Notes||
|MIStudio|ErgoTech|An intuitive drag-and-drop tool that lets you easily build secure Manufacturing Intelligence, Factory Automation and SCADA System. Design with one tool, deploy to Windows, Linux, J2EE, OSGi and headless embedded systems. View in any browser, on your PDA, or even on your Phone - any environment that supports a Java Applet.|http://www.ergotech.com/index.html|$2500|Web based (applets) so doesn't seem to be a licensing cost for deployment|Since it is applet, probably not going to work for us.  Looks heavily focused on packaged HMI, not really a general framework so that is not great.  Also did not see much in the way of support on their web site (no manuals, wikis, etc.)|
|GLG Toolkit|Generic Logic|GLG's extensive library of dials and meters, gauges, graphs, process control widgets and other graphical components is built on top of the Toolkit's object engine - an approach radically different from the traditional methods of creating programming components.|http://www.genlogic.com/components.html| | |This looks like a pretty nice option.  The have a widget catalog here: http://www.genlogic.com/widgets.html and probably would cover what we would use it for.|
|JSENT|JSENT|JSENT is a pure Java-based Supervisory, Control and Data Acquisition SCADA software product that runs on both Windows and Linux.|http://www.jsent.co.za/index.html|?| |This looks like an actual application so it really doesn't fit our needs|
|Factory PMI|Inductive Automation|A web-launched, database driven plant management interface suite. Featuring SQLTags. |http://www.inductiveautomation.com/products/factorypmi/|$3500|$0|This is a turn-key solution and really doesn't fit what we need.  Licensing would be OK and the delivery looks like JWS, but not sure how customizable it will be and probably cannot be integrated into our appliation.|
|JPC|Net Module|Easy to use (drag and drop) HMI development tool. Engineers without Java programming experience can build their HMIs. The product bundle 'JPC Framework' comprises the JPC Components 'JPC Client', 'JPC Server' and 'JPC Ambassador'. It is the basic product and you must acquire it when you start developing your JPC application. All other JPC Components are separate products.|http://www.netmodule.com/en/products/netmodule_jpc/|?|?|Looks like a large package really tailored to connect up with factory floor systems and provides a tool for drag-n-drop GUI building for HMI.  Probably more than we want and not sure we could break out the component from the GUI builder.|
|JViews Diagrammer|IBM (was ILOG)|ILOG JViews Diagrammer is the most comprehensive set of Java tools, components and libraries for creating graphical editing, visualization, supervision and monitoring tools. Both diagrams-displays used to show the relationships between objects-and dashboards-displays for monitoring business or industrial systems-can be easily created. |http://www.ilog.com/products/jviews/diagrammer/| | |One of the better frameworks out there, but costs were a bit of a nightmare to manage.  Maybe it is better now.  I have a request in to the guy that I worked with before and now that they are IBM, maybe things have changed|]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris P., Brent, Jim, Scott, Julie, Wayne, Gene, Roman, Chris S.


Absent: Doug P.
\\

h2. &nbsp;Issues:

1.&nbsp; Drifter cruise #2 has been moved from Aug 6 (tomorrow) to Aug 12 due to pressure and leakage issues of Mack. If Mack gets fixed, canning will take place next Tuesday.

2.&nbsp; Scott and Roman working to understand how/why pressure gauges moving out of calibration so much.&nbsp; Brent to run check on all machines to see what is going on with other pressure gauges.Scott to give Iridium tracker to Thom Maughin for integration onto Drifter buoy.

3.&nbsp; The patch Brent pushed down to NEO out at M0 is working.&nbsp; It has successfully run through 3 WCR with no evac issues.

4.&nbsp; Brent has been contacted by Ivory; WHOI wants to communicate with their ESP using Iridium.&nbsp; Transferring TIFF's will be very expensive.&nbsp; Should we perform a JPEG conversion?&nbsp; NO.&nbsp; Will got to 4x4 size and stay with TIFF's so data is still available in images.

5.&nbsp; Scott had good idea to build socket for small board for addition of ESD resistors on dwarfs.

6.&nbsp; MOE will get new software next week.&nbsp; Should be ready for science Aug 16.


h2. Notes:

1.&nbsp; As decreed by Don Anderson at WHOI and approve by all involved parties, the first commercial ESP instrument has been renamed ESPChris in honor of Scholin.

2.&nbsp; We will keep Cheri's laptop to run Solidworks, and one of her desktop machines will be reassigned to Roman.&nbsp; All others will be returned to the I.S. pool.

3.&nbsp; Newly ordered D-ESP CTD scheduled to arrive August 30.

4.&nbsp; Meeting next week with Kevin, Brian, Rich, Brent, Chris P, Roman, and Chris S. to discuss start of&nbsp; WHOI-MRI grant and software needed.&nbsp; Date/time still to be determined.


h2.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Kevin, Wayne, Jim, Doug, Brent, Cheri, Chris S., Scott

h3. Machine Builds

* Cores/MFB's:
*# MFB#2 goes on Betty.&nbsp; Thermally calibrated; working on slug positioning
*# MFB#3 goes on Gordon.&nbsp; Monika wrassling with to get it to work....
*# MFB#4 and #5 are from Mclane.&nbsp; Notice very sticky syringes.&nbsp; Cheri trying to whip them into shape.
*# Betty and Gordon are finished with cold-testing.&nbsp;
*# Moe is ready for the new box Jim S. has built. Box should be ready today.&nbsp; Cheri has&nbsp; few connectors to add to box top.

* Gordon and Betty both need new CBV lines.
* Brent mentioned problem Monika having w/ re-setting of valve; Scott will look into it.
* Chris interested in another board spin/population to sell to McLane.&nbsp; Looks like boards (spin, stuffed, tested(?)) are Core=$6K, MFB=$1.5K

h3. MFB


h3. Drifter&nbsp;


h3. Software

* Gordon to get the new GUI branch of software next week.&nbsp; Brent to talk to Monika.&nbsp; Perhaps they'll unhook MFB#3 and run a test protocol just to give Kevin some data.&nbsp; This should happen early/mid next week.

h3. Deep ESP/DWSM

* PISSer
** Doug building.&nbsp; Should be finished early next week.

h3. GUI


h3. Deployment Issues

* Sept 24 is next big surface deployment.&nbsp; Moe w/PCR will go at M0.&nbsp; Mack and Bruce, doing HAB work will be in the north Bay--locations to be determined by John Ryan.&nbsp; Slight move of antenna at Abe's house should hit M0 and north Bay.&nbsp; Will attend to when we know of n. bay location.&nbsp; Priority list is as follows:
**# Moe at M0
**# Betty on MARS
**# Bruce and Mack in N. Bay
**# Gordon on Pier deployment

h3. &nbsp;Other Items]]></property>
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<property name="body"><![CDATA[Short meeting.\\

Decided to heat entire sphere.&nbsp; This will be easier to build/control, and have positive impact on reagents as well as mechanicals.

&nbsp;Firmware Merger:

v 3.51 is on GG and MFB2

v3.54 is latest version will go on GG and MFB2.&nbsp; GG is a low-risk start.\\

Brent to give a brown-bag on how to configure servo motors.\\

Pressure sensors are in qeue to ship Aug 24.\\

Most parts for DWSM HP sampler are in and Doug is beginning construction.]]></property>
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<property name="body"><![CDATA[h3. Here are some commands to help ascertain the state of the ESP:

*Flush.location*
&nbsp;Shows where the flush puck is

*clamp.contains&nbsp; #PC* or *CC*
&nbsp;What puck the Clamp contains (if any)

*Storage.pucks.sort*
&nbsp;shows a sorted list of the number of pucks in each tube

*Storage.pucks\[tube#\]=nil*
&nbsp;Causes the software to forget how many pucks were in tube#

*Storage.pucks\[tube#\]=n*&nbsp; #where n is a number
&nbsp;Sets the number of pucks in tube# to n

*Storage.pucks\[tube#\]+=j*
&nbsp;Adds j pucks to the software's record of the number of pucks in tube#

*Storage.pucks.clear*
&nbsp;Causes the software to forget how many pucks were in all tubes

*Flush.to clamp&nbsp; #PC* or *CC*
&nbsp;A safer alternative to clamp.loadFlush

*Flush.garage*
&nbsp;A safer alternative to clamp.unloadFlush

*Arm*
&nbsp;Shows where the arm is

*Arm.owner*
&nbsp;Shows which thread owns the arm

*Flush.owner*
&nbsp; Shows which owns the flushpuck

*Arm.changeOwner Thread.current, :force*
*Flush.changeOwner Thread.current, :force*
&nbsp;Changes the owner of the Arm or FlushPuck to the current thread]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began?? and ended ~ week later when pump tore from piling.

*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).
Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

*Sept 25*

ESP-NEO returned after being stored in (un-airconditioned) shed, unopened since above date.&nbsp; Bleach had leaked and corroded all internal components.

h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays
Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

MELO used was #300034012090780

location reported by MELO was-\- &nbsp; 33.4865 \-118.51285

*March 20*\--lost comms

*March 21*\--re-established comms and think problem in E/M cable.

*March 22*\--lost comms

*April 3*\--small boat to buoy to test E/M cable

*April 8*\--'rescue' mission. Swapped E/M cables and repositioned in slightly deeper water, at 33.48504 \-118.50988

water depth 175m.&nbsp; top of can 10.9m

*RECOVERY--see below*

h4. {color:#ff00cc}ECOHAB--S. California{color}

*April 1*\--Instruments deployed

&nbsp;MOE--inshore at 33.60779 \-118.01877 with ISUS

Melo was 300234060014550

avg can depth \~9m
\\

&nbsp;Bruce--offshore at 33.58609 \-118.03686

Melo was 300234060016190

avg can depth \~19.5m

*~ April 9* lost communication with Bruce.&nbsp;

*April 15*\--Rescue mission w/Nerissa found 'hung' modem.&nbsp; Power cycled and checked cables on deck.&nbsp; Re-deployed in nearby spot.&nbsp; Divers (Kim R. & George M) measured 17.7m to top of can, 25.3 m to master link.

*RECOVERY*\--Plan was to pull ECOHAB April 30 with LBA0P divers off Nerissa, Catalina with Wrigley divers off Yellowfin May 1.&nbsp;&nbsp; April 30 had horrible Santa Ana winds; motored offshore to Bruce, and too rough.&nbsp; Cancelled entire day.&nbsp; Would try next day as winds supposed to die.&nbsp; Met at 5am and decided to cancel again, as winds were still blowing.&nbsp; Drove to Long Beach, and no wind up there. Salvaged that day by rounding up crew and wrigley divers after initially cancelling and heading over about noon.&nbsp; During that time, Dennis (skipper of Yellowfin) agreed to go the next day (Friday) to retrieve the two ECOHAB instruments.&nbsp; Eric Reinecker came down from MBARI, joining Jim Citanovich from SCMI and we retrieved Mack and Bruce.&nbsp; Back at SCMI around 1pm.&nbsp; Flatbed loaded by 4:30.&nbsp; Returned to MBARI next day (Saturday).

h4. {color:#ff00cc}Sulfur Cycling (Moran)--Monterey Bay{color}

*Sep 15*\--Instrument deployed

&nbsp;ESP-Gordon--at 36.83113 \-121.91114&nbsp; (M0) with ISUS and CTD.&nbsp; Forgot to start Melo (did it next day).&nbsp; Running archive-only mission, ended up deeper than we had hoped (~12m instead of 7-10m).

*Sep 18*\--Went out in Paragon w/ 2 divers (Eric R & Lisa Z.).&nbsp; Pulled \~0.5mi toward M0.&nbsp; Now at 36.83480 \-121.89800 at 5-8m.&nbsp; Sampling has resumed.

*Oct 15*\--Recovered all equipment. \\

h4. {color:#ff00cc}3G ESP Prototype flight on Makai{color}

*Nov 4*\--Makai deployed with one WCR cartridge.&nbsp; Surveyed area during that afternoon and morning of next day, fired cartridge.&nbsp; Recovered vehicle

*Nov 5*. ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Kevin, Wayne, Jim, Doug, Brent, Cheri,  Scott

h3. Machine Builds

* Cores/MFB's:
*# MFB #4 and #5 had wrong firmware which was causing the sticky syringes.

* RE: Monika having problem w/ re-setting of valve.&nbsp; Issue was that stand-alone software configuration had burkert positions opposite those of the integrated configuration.&nbsp; Now fixed.
* During cold testing of MOE, found that puck thermal sensor was corroded.&nbsp; Changing and recalibrating a new one is a nightmare; Cheri/Scott to work on building a jig that allows 'precalibration' of the finger sensor boards.
* Julie noticed that forearm not acting reliably--seems to be electrical connection cheri will fix.
* Must re-machine hand armature for new home sensor placement.
* Board boxes are here that we will use to send core board-set to McLane for their EPA build.

h3. MFB

* Brent has been wrestling with a firmware issue related to the PCR modules using a serial connection, and their inability to acknowledge recpt of an abort message.&nbsp; There is a relatively easy band aid if, using his serial port analyzer, Brent can't think of a better solution.

h3. Drifter&nbsp;


h3. Software

* Brent's firmware that runs motors is going very well.
* Noticed that his DWSM code has all polarities reversed because wiring in DWSM is reversed.&nbsp; We will keep the software intuitive and fix DWSM wiring ;&nbsp; Scott to check out what this entails.

h3. Deep ESP/DWSM

* High-pressure pump is finished and has been run at 200(?--low) pressure.&nbsp; Both bell housings are apart, and we will wait to put the tops back on until new transducers arrive Aug 24.&nbsp; PISSer should be ready for use with DWSM by end of week.
* Minor problem with blue oil bag; fitting broke inside; Doug will look at.&nbsp; Now using a bucket as the oil reservoir.
* All parts here for heater ring inside ball; Doug to hand-off to Jose.
* Sphere insulation is cut, but not installed.&nbsp; Doug to do.

h3. GUI

* GUI branch is running today (Chris P), and generating log data for Kevin to play with.

h3. Deployment Issues

* Sept 24 triple deployment.&nbsp; Moe at M0, Bruce at Santa Cruz, and Mack in 16m of water only 5-7m deep.&nbsp; Will needto adjust mooring for that one.
* Sep 30 is MARS.&nbsp; Brent has to give talk that evening so may not be on ship unless guaranteed to be back early.

h3. &nbsp;Other Items

* LabAutomation meeting in Palm Spring Jan 23-27, 2010.&nbsp; Must select who can/wants to go.
* R&D 100 award banquet Nov 17.&nbsp; Still working out logistics on who will go. ]]></property>
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<property name="body"><![CDATA[Materials for Accel cartridge testing
# [Cartridge assembly document from Accel|^Cartage Assembly Procedure.docx|cartridge build procedure]
# [BOM for Cartridge (v1), puck, and holders|^BOM MBARI 2013-09-17.xlsx|BOM]
# [Valve Movements Necessary|^Cartridge valve order nov 2013.xlsx|Valve movements]

h2. +Test Plan v1&nbsp; (Sep 13, 2013)+

Must label ports/paths on cartridges

Convention for syringes (with spool valve on left) will be:
|| 0 || 1 \\ || 2 \\ || 3 \\ || 4 \\ ||
| Spool valve \\ | check valve | check valve \\ | | |
| | spring | spring | | |
| | air | RNALater | waste | waste \\ |
\\
\\

h5.


h4. Filtration Speed and Evac

\--22 PSI thru puck within CARTRIDGEwithin Accel Test Holder

within G2 holderusing raw seawater, with x3 replica's

h4. Syringe Functions

\--How to load syringes

\--check valves; do they leak or hold pressure?

\-After Final Assembly Testing by hand:
\--define actuation process

\--build bench testing actuator

h4. Full Assembly sub-test&nbsp; (all testing will have companion G2 comparison test)

&nbsp;--filter

\--move spool valve

\--evac w/ push

\--remove puck and weigh

When procedure refined, run w/ 0.45 filter and filter 'stacks'

h4. Final Assembly Test (all testing will have companion G2 comparison test)

&nbsp;--filter

\--move spool valve

\--evac w/ push

\--hit with RNALater

\--remove and process filter [BOM MBARI 2013-09-17 ARCHIVE CARTRIDGE.pdf|^BOM MBARI 2013-09-17 ARCHIVE CARTRIDGE.pdf|Cartridge v1 BOM]]]></property>
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<property name="body"><![CDATA[h1. Engineering mtg

Present: Birch, Jensen, Roman, Pargett,  Preston, Marin, Gomes

Absent: Scholin, Everlove

h1. S. California

\\

1.&nbsp; Trip-planning
* Paul Dimeo of the Aquarium of the Pacific has been put in touch with Kim Reisenbechler RE: divers.&nbsp; Should have this nailed down by early next week.
* Scott contacted by George and Hai of OCSD.&nbsp; Apparently they needed proof of insurance and liability before allowing us on the roof.&nbsp; they've been directed to Pinto so we are good to go when we recover the antenna.&nbsp; They've made a request for one of them to attend the deployment.&nbsp; Would be very good politically to take one out with us.
* Coast Guard has told Mike Kelly we do NOT need a Notice to Mariners; there are already so many moorings out in that area that we are covered under one or more.&nbsp; Just let them know when we recover.
* We will load on Shana Rae, Thursday, March 25 at 10am.&nbsp; Jim will email Jim this info.&nbsp;&nbsp;
* E/M cables; both fabricated, now to start testing.&nbsp; Float material is being machined.&nbsp; Scott figuring out float spacing.
* new anchor line to arrive by March 24.

Deployment:
* Team will be Roman, Scott, Jim.&nbsp; Brent will be available via phone for troubleshooting (he leaves 9pm April 2)
* Still deciding best way to get equipment down to Newport Beach, but will leave Weds, March 31, load boat and deploy Apr 1, return to MBARI Apr 2.
* Will build a full dress of mooring in high bay before disassembling, so we know we have everything when we arrive down south.

h1. Other issues

A.&nbsp; Betty and hand problem
* hand still flaking and trouble-shooting is in stasis while Cheri in Falmouth and we prepare for deployment.

B.&nbsp; Doug--update on DWSM
* There is now power back to the core.
* New switches and ba adssembly in sampling can with serrated clips; hopefully no leaking now.
* Resample side has not been opened, but will open when kevlar gears come in.&nbsp; Then we'll replace switches in bag.
* Bill Ussler has seen DWSM and better understands what we mean when we say we depressurize water.&nbsp; He leaves on cruise tonight to test our wand fixture at the methane mound to see if depressurization causing clogging with precipitating hydrate.
* Need to double-check weights and&nbsp; space on WF.&nbsp; Find out how many hours from port the location is.&nbsp; this will help decide where we should open ball, should we need to.
* Some minor software development needed for wand--Brent/Doug/Scott to talk about before Brent leaves.
* Scott to talk to Pete G. about ISMS issues:&nbsp; batteries he's getting for us, which housing will we be using to mount to elevator.&nbsp; Must still mount computer in the ball.

C.&nbsp; 2G camera issue
* Original Starlight cameras were good
* Then came out with higher speed USB camera (f series) that did'nt work with our slower USB
* Now they have the r-speed, which seems to work at older, low speeds, but somtimes there are artifacts; restarting makes them go away.
* If our long term goal is to reduce power, Wayne has found board designed to work at 200mW (vs. 2.5W).&nbsp; We should use him to build a carrier board that would benefit both 2G and 3G systems.&nbsp; This goal is good, but will probably not be addressed until our deployment season is well under way.

D.&nbsp; Spending out of Moore Foundation $$
* Doug to get price for portable He leak detector
* Brent to get models/price for 4 HP computers, and old email about a cheap, low power radio to test
* Scott to get prices on 4 batteries and chargers for running cores in the lab.
* any remaining money will buy reagents through Roman and Chris P. ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris S., Brent, Bill, Scott, Doug, Jim, Chris P.

h1. Items


h4. Drifter

* ESP-Moe is machine for Hawaii.
* We will move our Pt. Lobos day from November (originally slated for MARS deployment) to August 10 or 11 for a drifter test-cruise.
* During that test cruise, we will use ESP-Mack, as brains and surrogate core.&nbsp; Moe will be 'on launch pad' and we don't want to jeopardize reagents with a canning procedure.&nbsp;
* We are moving closer on purchase of refrigerated van.&nbsp; Grech has a few final questions to vendor, making sure the van proposed can go on container ships.
* Final Drifter meeting before Brent leaves is TUESDAY, 10:30am after science mtg.
* h6. Drifter Science
* Must contact Julie to let her know MOE is ready (after checking with Roman)
* Will set up weekly science meetings to track preparation progress toward Hawaii

h4. WHOI

* Bruce still not recovered; we could not get boat for this weekend.&nbsp; Looks like June 10 is soonest to try.
* Chris saw the buoy bottom cone and said it looks like wrench marks on the cone and that the cable had been cut.&nbsp; Unclear, but we should think about overtly linking buoys with MBA (as people equate MBA and MBARI), given their Seafood watch program may be seen with suspicion by the fishing industry in the northeast. We need better Public Relations in the future, just in case, letting fishermen know what the instrument is doing.

h4. JdF Preparations

* Wand 'code' is very simple; on or off for two separate pumps.
* temperature probe on wand tip needs calibration validation.&nbsp; Bill to work with Brent on this this PM.
* ISMS and fixed temp probe to arrive from Harvard today or tomorrow.&nbsp; Will integrate next week.
* ISUS.&nbsp; Doug ordered him more 6-40 screws, but haven't heard from Luke.&nbsp;&nbsp;
* Now that we will have Iridium tracker decision is to use Acoustic Recall to return D-ESP to surface.
* Chris P. has workable mission script.
** Testing still needed:
**# Test temp probe calibration and validate.
**# Test low voltage code (turn stuff off before we run out of juice)
**# Test sampling at cold temperature
**# move code to flash memory
**# run (3?) full phases
**# communications path

* Decision is to close sphere on Thursday, June 9 before Scott leaves on the 10th for vacation.]]></property>
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<property name="body"><![CDATA[Present:&nbsp;&nbsp; Chris P.,&nbsp; Jim, Chris S., Bill

Absent: Julie, John R., Roman

{color:#3300ff}1. Machine Updates:{color}\\
* {color:#3300ff}NEO (at M0){color}
** {color:#000000}had a seg fault error this morning.&nbsp; Chris P restarted.&nbsp; Will see if it makes it to recovery on Monday.{color}

* {color:#3300ff}Mack{color}
** Chris tested at new pressures (55psi for SH1, 40psi for WCR), and pucks look good at these pressures.&nbsp; These are what we'll use during the CANON cruise.
** Gene to get Mack for Drifter installation on Sept 3.&nbsp; Some issues with drifter's batteries; unknown if enough power left to run for 5 days.&nbsp; Plan has always been to run for 3 contiguous days, 5 if we are lucky.&nbsp; Power used in the last 3 one-day test deployments is unknown, so we may purchase fresh batteries for drifter before CANON.
** Boat (WF) will be loaded late in day Weds, Sept 8.&nbsp; Chris needs tarp and sump pump to keep can cool.
** There will be a meeting today @ 3pm w/ Duffy to discuss where stuff will go on the ship.

* {color:#3300ff}MOE{color}
** Still needs software changes.
** Scott will integrate MFB1 into MOE
** Vanessa bck on Monday the 30th and will want to start working with her assays on MOE.

* {color:#0000ff}Bruce{color}
** DA testing still messed up.&nbsp; looks like a pressure or passive leak.&nbsp; maybe Scott can look into before Roman gets back?

* {color:#0000ff}Chris P PCR Paper progress{color}
** We will meet Tuesday, Sep 7 to generate some momentum]]></property>
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<property name="body"><![CDATA[Present:&nbsp;&nbsp; Brent, Jim, Scott, Doug, Chris P, Roman, John R., Julie

Absent: Chris S.

h3. Announcements:

1.&nbsp; OTIC kick-off meetings will be Nov 11 and Jan 13.&nbsp; Clem Furlong and the UW crew will be here both days.&nbsp; Laurie Connell and Greg Doucette will come in Jan.&nbsp; Annette handling travel/lodging arrangements.

2.&nbsp; Quick review of where to charge hours.&nbsp; Most work is now going on .00 sub-projects, except for occasional things Doug P is doing.&nbsp; Email went out detailing who charges what.&nbsp; If you weren't notified and you need to charge SURF Center, time goes on 900915 or 900913.&nbsp; Check with Jim.

h3. Issues:

* John R brought the LISST for show-and-tell, and discuss mounting options on one of the surface moorings (bight or shadow) during BIOSPACE.&nbsp; Looks like it will fit in the ISUS position with relatively little modifcation.&nbsp; Doug to get diameter before John sends back for calibration, John to get in-water weight and collect battery housing.

* Strain Relief.&nbsp; The strain relief on the can end of drifter appears to have failed.&nbsp; It again appears to be a manufacturing flaw.&nbsp; Scott thinks it will make it through tomorrow's deployment, but should be replaced before CANON cruise.&nbsp; Jim will check with Dale/Scholfield whether there is time to reterminate before CANON.&nbsp; We will use the recently rec'd new strain relief and again send this one back.

* Brent rec'd the 8MB board from McLane, and the 16MB they had ordered and shipped here.&nbsp; He quickly ascertained the problem and notified Ivory, who is on vacation until next week.&nbsp; This episode has Brent believing he needs better access to their network; things can be fixed from here, instead of fed-exing back and forth.

* New camera testing.&nbsp; Images look good, but anything coarser than 2x2 binning will show a pixel shift, due possibly to our slow processor.&nbsp; Chris P and Roman said 4x4 binning no longer used, so this is moot point.&nbsp; Brent will do a cold test, but this new camera (Starlight model 'R') is looking good.

* Pressure issues:&nbsp; Thanks to work of chris P., we have settled on pressures that 'work':&nbsp; {color:#ff0000}{*}55 psi for SH1, 40 psi for WCR{*}{color}. &nbsp; All machines will be changed to these, and Doug is looking at the availability of springs that, instead of being 2x current strength, may be only 1.3-1.4x.&nbsp; Increasing spring strength has consquences of ball screw selection and connection to the motor.&nbsp; All permutations being evaluated.&nbsp; We need to get this info to McLane as soon as we see how stiffer springs function.

* Cheri's computers.&nbsp; Will back-up her desktop harddrive, then use that machine as a replacement for Bufflehead.&nbsp; Her laptop (with Solidworks) will remain in lab (probably with Roman).

* MARS wet-mate connector being worked on.&nbsp; Scott thinks 10' section is long enough; will discuss with ROV pilots before formally placing order.

h5. +Machines+


h6. Bruce

Tina's assays were not working.&nbsp; Roman ran several from 2008; they worked perfectly.&nbsp; thought was something in the filter media could be causing issue.&nbsp; But then Roman ran more of Tina's this morning and it worked.&nbsp; We will continue to run Bruce up until BioSPACE to ascertain the problem.

h6. Mack

Mack is working.&nbsp; Connector on PSV seems no longer flakey, and with the lowered puck pressures and recalibrated pressure sensors, we are ready to can today, mounting on Drifter tomorrow AM.&nbsp; Roman taking out tomorrow for 3rd test.

h6. MOE

Ready for running.&nbsp; MOE should get the very latest software, which was a check to keep heaters from heating to temperatures that could never be reached.

h6. NEO

currently in water at M0. will get latest firmware when recovered (Aug 30)

Must decide what Science wants to do with NEO.&nbsp; Will there be a pier  deployment in Oct/Nov, and do we rid NEO of the tombstone and replace  with an MFB and the attendant firmware upgrades, so all cores will be  running the same thing?&nbsp; Discuss this at next Tuesday's science mtg.

h6. Gordon

Still in the ball.

h6. Betty

may become testbed for clamp spring testing.

h3. Communications for BIOSPACE

Scott heading to Abe's house next Tuesday (Aug 24) give him his 2010/2011 check, and oversee the antenna post install for this new antenna.&nbsp; He'll call Abe and antenna guy on Monday to confirm.]]></property>
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h4. JdF

* &nbsp;With the issues of Harvard's primers, we have decided to install the core into the Ball Tomorrow.&nbsp; No use waiting for their primers to be tested, as nothing seems to work.
* Will set up CTD with the RTD pass-through on *Tuesday* so we can test the wand temperature code before Brent leaves.&nbsp; Scott has seen that voltages get passed through the CTD, but haven't been able to do any more extensive testing.
* ISUS and ISMS are supposed to be ready June 1.&nbsp; Doug has spoken with Luke, and we will use their 2000m rated probe heads.&nbsp; The chamber water must flow through is quite small, which will restrict flow to all instruments downstream, using our new wand flow setup.&nbsp; Thus, will mount ISMS in parallel to ISUS; Doug figures 80% of flow will go through ISMS, rest through ISUS.
* Satellite Beacon on D-ESP.
** Issue:&nbsp; If ship must leave ESP and while we're gone, D-ESP rises to surface.&nbsp; Current radio link is for close proximity only (1-2mi).&nbsp; Several Options:

*# Make recall of D-ESP only with ROV pull release, no acoustic drop-wt recall.&nbsp; This several lessens chance of unintended lift-off.&nbsp;
*# Could mount ARGOS beacon to elevator.&nbsp; Ken Smith may have one we could borrow.&nbsp; Will ask when they return tomorrow.
*# Could mount Iridium tracker to elevator.&nbsp;

*** Both ARGOS and Iridium cost \~$4K, and have a small monthly data-plan charge.

h5. Travel Plans

* &nbsp;Arrivals to Newport:&nbsp; Chris P getting there July 8, engineers getting there July 9 or 10.&nbsp; MOB the 11th.&nbsp; Shove off 12th.
* Departures:&nbsp; We've been told ship will return to port at 4pm, July 23.&nbsp; Probably not enough time to unload and make it back to Portland that day given the afternoon arrival.&nbsp; Teresa says we will be allowed to remain on ship the evening of the 23rd.&nbsp; Thus, de-mob on 24th, and make return plans for that day.&nbsp; Bill staying until 25th to load truck and see equipment off.

h4. WHOI

* The ESP Bruce story being told [here|2011 Deployments].&nbsp;
* WHOI working feverishly to finish ESP-Chris mount and to test their buoy.&nbsp; Should know how/if it works by middle of next week.]]></property>
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<property name="body"><![CDATA[Present: Jim, Roman, Chris P., Julie, Bill

Absent:&nbsp; Chris S., John

{color:#3300ff}1. Updates:{color}\\
* {color:#3300ff}Moe in      cold room---plan for mid-April deployment?{color}
** Will use NEO for April 14 deployment.&nbsp; Julie to dust it off this week, and next week will discuss where NEO is in preparation for the deployment.
** Probes on Moe:&nbsp; currently using 1 NED (IPC), 2 FAM, rest TAM.&nbsp; So far only 1 positive FAM, and several inhibitions on all channels.&nbsp; Will continue the cold-room test for at least 10 more days.
** Roman giving Julie some deep water collected yesterday.&nbsp; May not have the inhibition that the surface water has.

* {color:#3300ff}Bruce      and DA.&nbsp; Software      Switched?&nbsp; Are we good to go?{color}
** Bruce code was changed to latest (new) code yesterday.&nbsp; Roman firing off&nbsp; a DA today as a final check.

* {color:#3300ff}Array      printing update?{color}
** All tips are working and Roman/Nilo have printed 84 DA arrays.&nbsp; Will QC these this morning; if fine, then Chris P., gets Nilo to start printing the more difficult (longer) BAC arrays.

* {color:#3300ff}PCR      reagents on Gordon---Chris P. update.{color}
** Chris P. to remove reagents this morning.

* SPE      columns---still waiting on quote.
* Chris P. still to check/confirm the IPC order.&nbsp; Sent in the PO, but did not hear that they rec'd it...

{color:#3300ff}2. Progress update on papers:{color}\\
* Chris      P.
** Discussed the Figures; much progress made.&nbsp; Chris will have rough draft of all figures by next week.&nbsp; Much discussion about what should be used to normalize arrays, background or other spots.&nbsp; She will try using several methods.

* John      R.&nbsp;
** Report from John:
*** \* BAC:
Working with Chris P. on environmental data to present in her paper

* \* HAB:Nilo and Roman have begun the process of turning array spot intensity into numbers for '08.&nbsp; I stand ready to assist in that processing, if needed, and I am ready to carefully examine how the significant patterns in the HAB time-series relate to the environmental variability (data from moorings, AUV, satellite).&nbsp; The interannual picture was mostly roughed out already, however I furthered the analysis by quantifying wind and hydrographic conditions of the '07 and '08 network deployments as anomalies (deviations from their climatological monthly mean).&nbsp; For example, this showed September '07 to be anomalously weak upwelling, and October '08 to be anomalously strong upwelling.* \* ZOO:Working with Julio on ESP and AUV results for his paper.]]></property>
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<property name="body"><![CDATA[Present:&nbsp;&nbsp; Jim, Scott, Doug, Chris P, Chris S.

Absent: Brent, Roman, Julie

h3. Announcements:

1.&nbsp; Bruce Kiefer arriving Sept 13-Oct 2, to learn end-to-end deployment procedures.&nbsp; Don Peters from EOM also coming for a day to observe.

2.&nbsp; Vanessa here from Aug 30 to Sept 20

3.&nbsp; Liz O. will be here in Sept for cruise(?)


h3. Issues:

* Pressure issues on all cores.
** We believe we've found the problem, which seemed to have become exacerbated when we added the larger o-ring in the PEEK. This gave the puck more surface area to 'push back' on the clamp, and we were operating near the capacity of the springs, thus the pucks would leak/not hold pressure.&nbsp; The fix is relatively simple.&nbsp; Doug has chosen some springs to 'double-up' above and below the puck, and we will go to a softer aluminum coupling b/w motor and ball screw.&nbsp; This pressure issue is only and issue with the fine porosity filters, which are not used in HAB operation, so it is not a critical path issue for McLane, although something they will be notified about.
** Moe will go through it's final check-out next week, and if the current SH1 and WCR pressures work, we will not exchange any springs until after the BIOSPACE deployment.

* E/M cables.
** We currently have 2 'long' and 3 'short' EM cables:
*** LONG
**** one 22m cable is currently on Drifer
**** one 20m cable has an incipient bird-cage near the middle (6m) and needs the bending strain relief (BSR) repaired.
*** SHORT
**** two 15m cables (currently one is deployed w/ NEO, one is here at MBARI)
**** one has end cut off to fix BSR
** We must repair one (to have 5 cables); Scott will decide Monday after talking to Gene/Paul.
** {color:#cc0000}We need to purchase more cable this winter.{color}

* ISUS
** Drawings for ISUS 4K housing are finished and have been checked by Ray (thanks Doug).
** Will have a meeting with Ken Johnson and Luke to approve.
** Also need to discuss what equipment SURF has and wants them to build, so we only need to tap the Johnson group once/year for calibrations.
** Meeting slated for Tuesday, Aug 31, 11am.
** Must also figure out how to power ISUS.&nbsp; Using ESP batteries saves us from $15K battery housing, but does it run off a power converter?

* Spares
** Unknown what spares we have and/or where things are located in the lab.&nbsp; Waiting for Roman to return from vacation and we will do major reorganization, and possible re-order of parts, in particular spare PTV and CTV's.

* Antenna at Abe's house has not been mounted, as it did not arrive on Monday.&nbsp; Scott will work next week to schedule another time.&nbsp; Unlikely to work mounted on fascia.

* MARS wet-mate connector PO (#*1011191)* approved today.

h5. +Machines+


h6. Bruce

Scott and Jim worked on PTV, finding that it does not hold pressure.&nbsp; Found an old used PTV; disassembled, both look similar.&nbsp; We swapped rotors and are pressure testing this combination over the weekend.

h6. Mack

All reagents are on (except HAB/DA).&nbsp; Chris will run WCR/Bac/WCR&nbsp; with runs through the weekend.&nbsp; Monday is puck-fest.&nbsp; Load them on Tuesday, can on Weds and give to Gene on Thurs/Friday.&nbsp; That is also the day of the post-can QC.&nbsp; Drifter gets loaded on Weds, Sep 8.&nbsp; Chris to assemble materials to keep Mack cool.

h6. MOE

Scott fixed broken traces on collection temp sensor.&nbsp; Chris doing series of runs over weekend, getting ready for Julie handoff.

h6. NEO

currently in water at M0. will get latest firmware when recovered (Aug 30).&nbsp; Jim and Scott to get Monday am. 6:30 for 7:00.

h6. Gordon

Still in the ball.

h6. Betty

no report.

h3.]]></property>
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<property name="body"><![CDATA[Present: Jim, Chris S., Wayne, Brent, Doug, Cheri, Scott, Jose
Absent:&nbsp; Addie (maternity)

h3.


h3. Machine Builds

* &nbsp;Two new cores are being kitted by Cheri.
* Syringe and rotary valve parts were inadvertently left off original (July) El Camino order.&nbsp; Mike P. pushing those through and should be ready by Jan 23.
* Discussion on McLane visit for core builds.&nbsp; Decided to have them reserve 2 weeks; Feb 8 and Feb 22.&nbsp; If they really work the first week, maybe stay longer and make it just one trip out.
* Cheri has drawing of new harmonic drive mount.&nbsp; We need it manufactured.&nbsp; Will talk to Mark Brown about getting some (Non-Mike Parker) help.
* Cold syringe testing.&nbsp; Not finished.&nbsp; Deadline is when we put a core in the sphere (late March).
* Next two Sleepy core boards need names.&nbsp; Cheri will spearhead that effort.
* Pucks.&nbsp; Chris S. wants to revisit high-volume puck issue and the machining of scintered frits.&nbsp; Several solutions batted around.&nbsp; Chris will look for HV pucks and we will discuss next week.
* We will integrate MFB01 with Moe the week of Feb 1.
* Scott tyring to get a workable ORCAD part number scheme to keep track of our wiring harnesses.&nbsp; Working on this with Jose.
* MOE is the CMORE/Moore/NSF machine that will go to Zehr lab and run in surface waters at M0.
* Who goes into sphere?&nbsp; Initial tests do not require PCR, so Mack or Bruce could do it.
* In June we could put NEO in sphere--must decide thi in April.


h3. MFB

* &nbsp;Cheri will work on kitting up the 7 MFB's for the McLane build.&nbsp; She should be able to ship them by first week in Feb.&nbsp; Chris will call and give them a heads up to expect the kits.
* Some question as to whether we cut tubing, or Mclane does it.&nbsp; Has that been included in their $4500/each quote?

h3. Software

* &nbsp;CTD bug.&nbsp; still a longstanding bug.&nbsp; Brent given problem to Bob Herlien, who know says he doesn't have time to work on it.&nbsp; Brent thinks he'll need 3-5 days.&nbsp; Jim to check to see if he can even do it.
* Bufflehead is moving to the lab to give Brent some more space in his office.
* NEO--running old Ruby code with newly patched Ruby compliler.&nbsp; Moe has latest Ruby with same newly patched compiler.
* Decision to keep NEO it's own little old island of code, but upgrading \~1mo before it may be deployed.&nbsp; This will allow Chris P. to continue with MFB work without changing anything (or having anything break).
* Wayne has all CPLD code cleaned up and into CVS.&nbsp; He's also built many more test benches.&nbsp; Monday will be picking up on MSP430 software development.
* &nbsp;

h3. DWSM


h6. +Sphere+

* &nbsp;All connectors are in for the sphere.&nbsp; We will move it to Bellingham AUV lab Monday for install.&nbsp; Plan is still to get it shipped to SRI late next week.
* Decision is to ship it *{+}disassembled{+}*.

h6. +Elevator+

* &nbsp;Mike Parker waiting for solidmodel from Doug.&nbsp; Will send today.
* Currently, elevator has no legs.&nbsp; Doug has designed 6 8" standing legs, and 3 adjustable legs for ocean bottom landings.
* Adjustable legs being&nbsp; designed for up to 20 degree slope.
* Jim will talk to Mark Brown about getting Mike Conway help on drop-weight design.

*{+}DWSM{+}*
* &nbsp;Mechanically, DWSM is 95% complete.
* Software interface still needs design and many electrical connectors/cables to order.&nbsp; Brent and Scott are on it.&nbsp; They will meet with Doug to create config file that is usable for testing.
* Cable connection;&nbsp; we need a short one to connect to ROV, longer (80m?) to connect to MARS.&nbsp; Craig Dawe may be able ot help with this; connectors have long lead time.&nbsp; Scott to talk to Craig, Jim to Etchemendy.

h3. GUI Development

* &nbsp;no developmentts reported

h3. Other Items:

* &nbsp;Next week will have two off-line mtgs:
** Scott, Brent, Jim, Chris, and Gene to discuss drifter integration
** Brent, Jim, Chris, and Kevin G. to discuss GUI development]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision
# [25Jun2009]
# 02Jul2009 - no meeting; 4th of July break
# [09Jul2009]
# [16Jul2009]
# [23Jul2009]
# 30Jul2009 - Scott ran mtg; proposal preparation
# [06Aug2009]
# 13Aug2009 - cancelled; proposal/grant preparations
# [20Aug2009]
# 27Aug2009 - Jim Vacation; Scott in charge
# 03Sep2009 - Jim Vacation; Scott in charge
# [10Sep2009]
# [01Oct2009]
# [08Oct2009]
# [15Oct2009]
# [22Oct2009]
# 29Oct2009 - Jim LLNL;Engineering & Chris S. set-up schedule for next MARS
# [05Nov2009] \-meeting of all ESP team on 03Nov
# 12Nov2009 - R&D 100 Awards in Orlando
# [19Nov2009]
# 26Nov2009 - Thanksgiving]]></property>
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<property name="body"><![CDATA[Present: Birch, Jensen, Roman, Pargett, Preston, Marin, Everlove, Scholin

Absent: Ryan

h1. S. California
\\

1.&nbsp; Pre-trip:&nbsp; Will be week of March 15.&nbsp;
* Probably Tuesday, March 16.&nbsp; Birch/Jensen/Roman
* Will fly into John Wayne Airport, but waiting to hear answers to many questions from Burt/Matthew.
* Will take Shana Rae.&nbsp; Load mooring gear on Thursday, March 25 in Moss Landing, then drive ESP's down in van on 30th.&nbsp; Load on ship on 31st.&nbsp; Deploy April 1.
* Divers. Looking into using local divers.&nbsp; Doug Conlin has contact with local UCLA group.&nbsp; Brent also has some leads.
* Moorings:&nbsp; Jims Scholfield should have them finished by March 17.&nbsp; Training Paul C. while he makes these two.
* Foam blocks arrive March 29.&nbsp; We will scavenge from exisiting E/M while these blocks are out being machined.&nbsp; Will end with 3 'short' and 2 'longer' E/M cables.
* Batteries arrive March 10 and be assembled by March 17.
* Will need new anchor lines but need to verify depth

h1. Other issues

A.&nbsp; Betty and hand problem
* Betty is not deployable.&nbsp; We cannot recreate the problem (presumed to be a short somewhere) to know where to test/what to replace. Vexing.&nbsp; Will continue to exercise the hand, hoping that use will cause failure....

B.&nbsp; Doug--update on DWSM
* Problem was that we weren't reliably able to see empty or squeeze, so we didn't know when to stop pumping.&nbsp; We could change the code to look for a current increase in the pump, but that's kind of a hack.&nbsp; Doug to test for another week, then power down to allow Scott access to battery box in order to cast a new one.
* Before that, Chris P. will clean Gordon Lines and remove reagents.


C.&nbsp; Cheri--MFB build update
* MFB builds continue.&nbsp; hope is to have all finished before she leaves for Mclane (March 15).&nbsp; MFB distribution list is [here|ESPAPP:MFB-PCR distribution list|Who gets which MFB].

D.&nbsp; Next MFB training will be week of May 24.&nbsp; Will distribute MFB's in June.]]></property>
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<property name="body"><![CDATA[Present: Chris P., Bill, Jim, Chris S., John, Roman

Absent: Julie
\\

{color:#0033ff}1.&nbsp; Move ESP mtg time to accommodate CANON?{color}
* CANON meets every other Tuesday from 10-11.&nbsp; We will move ESP Science meeting.&nbsp; New time: 9-10am every Tuesday.&nbsp; Surface Commons.

{color:#0000ff}2.&nbsp; Updates:{color}
* Moe is in cold room and Chris will start running while Julie is on vacation this week.
* Puck giving blow-back, which allowed less and less reagent in.&nbsp; Roman has changed code and Bruce has run good DA's.&nbsp; Roman will move that code onto Mack (running latest Ruby) and see.&nbsp; ({color:#ff0000}3-4-10 update{color}:&nbsp; it works\!.&nbsp; Will use old DA code in new Ruby machines).
* Array printing.&nbsp; No message from Nilo, so unknown if cavro was installed this weekend.&nbsp; We will start printing with tips we have.
* Gordon reagents.&nbsp; It's set-up so it COULD run, but if we are serious, we should reload.&nbsp; Deemed lower priority given the S. Cal trip coming up.
* We should order more SPE columns.&nbsp; Addie ordered them last, lookup in PO's.&nbsp; We think from company called Column Engineering.

{color:#0000ff}3.&nbsp; MFB Traning?{color}
* There will be a training for water quality monitoring people in April after M0 deployment.&nbsp; SCCWRP, USC, MLML will each send 1 person.&nbsp; Stanford maybe 2 people.
* Purpose is introductory MFB training, then a referee session to determine who is doing what.
* Ali Boehm will get a COS post-doc that will come down for training.
* priority list on who gets MFB's is [here|ESPAPP:MFB-PCR distribution list|PCR distribution from MBARI].

{color:#0000ff}4.&nbsp; DA reagent schedule.{color}
* Chris S to check with Greg about DA production schedule.
* propose to get DA reagents March 23.

{color:#0000ff}5. S. California deployment{color}
* no archiving during this deployment
* will take Shana Rae.  Use local divers.
* Discussion ensued about how to move instruments.&nbsp; Decided to have SR pick up mooring material on March 26.&nbsp; We drive two cans down on 30th and mount on 31st for April 1 deployment.]]></property>
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<property name="body"><![CDATA[h3. Distribution list as of 4 Nov 2010:

\\
\\
|| MFB || PCR Module # || on Core || who gets? || ||
| tombstone | 5 \\ | NEO \\ | MBARI | |
| MFB1 | 1 | Moe | MBARI | |
| MFB2 | 12 \\ | \\ | {color:#006699}slated for{color} CMORE (UCSC) | |
| MFB3 | 4 | Gordon | MBARI | |
| MFB4 | \\ | \\ | no heater block; no PCR module\\ | |
| MFB5 | 7 \\ | Betty | MBARI \\ | |
| MFB6 | 8 \\ | | At SCCWRP (S. Cal) | \\ |
| MFB7 | | | {color:#006699}slated for{color} Harvard/Girgius;&nbsp; no ARV motor, no PCR module\\ | |
| MFB8 | none | | At Stony Brook, NY (Harbans Dhadwal) | |
| MFB9 | 13 \\ | | At Caltech/Orphan | |
| MFB10 | 11 | | At Stanford (Ali Boehm's lab) | |
| {color:#000000}&nbsp;MFB11{color} | 14 \\ | | MBARI; \\ | \\ |
| | | | | |
| | Spares:&nbsp; none | | | |
| | \\ | | | |
| | Broken?: | | | |
| | 3 | | was originally on Tombstone, but moved #9 there for M0 deployment. Not enough sensitivity.&nbsp; \\ | |
| | 10 | | removed from MFB6.&nbsp; Bleach leak caused flakey connector. \\ | |
| | 9 | | removed from tombstone.&nbsp; Erratic diode readings \\ | |]]></property>
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<property name="body"><![CDATA[In order to read in data from the ESP, the GUI will use the ESP's log (*real.log*) file as the official 'interface' for data collection.  In order to facilitate this, this page documents what the entries in the log file should look like so that the ESP GUI will not have to make extensive and fragile rules to try and interpret the data.  The esp gui log data should have the following format in the context the [raw log file|ESPAPP:Parsing the Raw ESP Log File Format|Raw Log File Format]:

_EVENT-NAME{_}*,*{_}attribute=value,..._

Notes:
# Time is designated using epoch seconds (number of seconds that have elapsed since January 1, 1970) in _GMT_
# EVENT_NAME is one of the following:
## BEGIN_MISSON
## PHASE_START
## PHASE_END
## PROTOCOL_START
## PROTOCOL_END
## SAMPLE_START
## SAMPLE_END
## CAMERA_SNAP
## END_MISSION
# Attributes are key=value pairs and vary from event to event.  Attributes for the various events are:
## BEGIN_MISSON
### No attributes
### Example: {{BEGIN_MISSION}}
## PHASE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### Example: {{PHASE_START,phase_name=hab}}
## PHASE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS (this is the time that the phase started.  This is necessary due to the fact there are multiple threads the name & start date are the unique key.)
### Example: {{PHASE_END,phase_name=hab,phase_start=1231372399}}
## PROTOCOL_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECDONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### Example: {{PROTOCOL_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1}}
## PROTOCOL_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### Example: {{PROTOCOL_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399}}
## SAMPLE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### target_volume=ZZZZml
### Example: {{SAMPLE_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,target_volume=1000ml}}
## SAMPLE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### sample_volume=ZZZZml
### Example: {{SAMPLE_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,sample_volume=934.1ml}}
## CAMERA_SNAP
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### file_name=ZZZZZZZZZ.tif
### auto_exposure=AAAAAAAs
### Example: {{CAMERA_SNAP,phase_name=hab,phase_start=1231372399,file_name=bac08oct1716h450ml40s.tif,auto_exposure=123.4s}}
{panel:title=Actual log entries}
Rich made the changes to the ruby code to generate the log entries in the following format:
# protocol/BAC.rb
## Thread.log.data "BAC_BACSH1_START"
## Thread.log.data "BAC_BACSH1_START"
## Thread.log.data "BAC_SHORTBACSH2_START"
## Thread.log.data "BAC_SHORTBACSH2_END"
## Thread.log.data "BAC_PHASE_START"
## Thread.log.data "BAC_PHASE_END"
# protocol/samplepass.rb
## Thread.log.data "SAMPLEPASS_LYFIL_START"
## Thread.log.data "SAMPLEPASS_LYFIL_END"
# protocol/PUFM.rb
## Thread.log.data "PUFM_START"
## Thread.log.data "PUFM_END"
## Thread.log.data "PUFM_WITHINITIALPURGE_START"
## Thread.log.data "PUFM_WITHINITIALPURGE_END"
# protocol/HAB.rb
## Thread.log.data "HAB_HABSH1_START"
## Thread.log.data "HAB_HABSH1_END"
## Thread.log.data "HAB_SHORTHABSH2_START"
## Thread.log.data "HAB_SHORTHABSH2_END"
## Thread.log.data "HAB_PHASE_START"
## Thread.log.data "HAB_PHASE_END"
# protocol/wcr.rb
## Thread.log.data "WCR_PROTOCOL_START," + " volume=#\{sampleVolume\}"
## Thread.log.data "WCR_PROTOCOL_END"
# protocol/DA.rb
## Thread.log.data "DA_DAEXTRACT_START"
## Thread.log.data "DA_DAEXTRACT_END"
## Thread.log.data "DA_START"
## Thread.log.data "DA_END"
## Thread.log.data "DA_SHORTDA_START"
## Thread.log.data "DA_SHORTDA_END"
## Thread.log.data "DA_HAB4DA_START"
## Thread.log.data "DA_HAB4DA_END"
## Thread.log.data "DA_HABDA_START"
## Thread.log.data "DA_HABDA_END"
# protocol/utilities.rb
## Thread.log.data "PROTOCOLARGS, assay=#\{opts\[:assay\]\}, maxvolume=#\{sampleVolume.first\}, wcrmaxvolume=#\{sampleVolume.last\}"
## Thread.log.data "INITIALPURGE_START"
## Thread.log.data "INITIALPURGE_END"
## Thread.log.data "FINALPURGE_START"
## Thread.log.data "FINALPURGE_END"
# protocol/LARV.rb
## Thread.log.data "LARV_LARVSH1_START"
## Thread.log.data "LARV_LARVSH1_END"
## Thread.log.data "LARV_SHORTLARVSH2_START"
## Thread.log.data "LARV_SHORTLARVSH2_END"
## Thread.log.data "LARV_PHASE_START"
## Thread.log.data "LARV_PHASE_END"
## Thread.log.data "LARV_PHASE_WITHPURGE_START"
## Thread.log.data "LARV_PHASE_WITHPURGE_END"
# protocol/sh2.rb
## Thread.log.data "SH2_PROTOCOL_START"
## Thread.log.data "SH2_PROTOCOL_END"
## Thread.log.data "SH2_SHORTSH2_START"
## Thread.log.data "SH2_SHORTSH2_END"
## Thread.log.data "SH2_SH2CORE_START, phase=#\{phase\},label=#\{label\}"
## Thread.log.data "SH2_SH2CORE_END"
# protocol/sh1.rb
## Thread.log.data "SH1_PROTOCOL_START"
## Thread.log.data "SH1_PROTOCOL_END"
## Thread.log.data "SH1_COLLECTSAMPLE, " + "volume=#\{sampleVolume\}, bubblepoint=#\{collectionSampler.bubblePt\}"
## Thread.log.data "SH1_COLLECTSAMPLE_COMPLETE"
## Thread.log.data "SH1_LYSING, volume=#\{lysisVolume\},solution=#\{lysisSolution\}"
# protocol/MFB.rb
## Thread.log.data "MFB_MFBSH1_START"
## Thread.log.data "MFB_MFBSH1_END"
## Thread.log.data "MFB_START"
## Thread.log.data "MFB_END"
# protocol/KAR.rb
## Thread.log.data "KAR_KARSH1_START"
## Thread.log.data "KAR_KARSH1_START"
## Thread.log.data "KAR_SHORTKARSH2_START"
## Thread.log.data "KAR_SHORTKARSH2_END"
## Thread.log.data "KAR_PHASE_START"
## Thread.log.data "KAR_PHASE_END"
# lib/esp.rb
## Thread.log.data "LIB_ESP_IRB_START, string=" + $0
## Thread.log.data "LIB_ESP_CONFIG,instrumentname=#\{Name\}, cfgpath=#\{ConfigPath\}"
## Thread.log.data "LIB_ESP_IRB_END" 
## Thread.log.data "LIB_ESP_APPLICATION_START, string=" + $0
## Thread.log.data "LIB_ESP_CONFIG, instrumentname=#\{Name\}, cfgpath=#\{ConfigPath\}"
## Thread.log.data "LIB_ESP_APPLICATION_END" 
# lib/cmdserver.rb
## Thread.log.data "LIB_CMDSERVER_ABORTMISSION" + reason
## Thread.log.data "CAMERA_SNAP, " + "string=#\{instance\}: #\{SNAP\} #\{args\}"
## Thread.log.data "CAMERA_OUTPUT_" + myn.to_s + ", string= " + line 
{note}
above should expand to:
{noformat}
      CAMERA_OUTPUT_1, string=Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
      CAMERA_OUTPUTA_2, string=Exposing 348x260 pixel 16-bit image for 25.668 seconds
      CAMERA_OUTPUT_3, string=/var/log/rich/larv07oct3015h50ml2.5s.tif: TIFF Upload Complete
{noformat}
{note}
# utils/puckmoves.rb
## Thread.log.data "PUCKMOVES_LOADCLAMP, " + 
{note}
above expand to: 
{noformat}
PUCKMOVES_UNLOADCLAMP, source= , pucknumber= ,tube= , clamp=
{noformat}
{note}
## Thread.log.data "PUCKMOVES_LOADCLAMP_EMPTYTUBE, tube=#\{tube\}"
## Thread.log.data "PUCKMOVES_UNLOADCLAMP, " + guiMsg % \[source.label, clamp.name, toTube\]
{note}
above expand to: 
{noformat}
PUCKMOVES_UNLOADCLAMP, source= , clamp= , tube=
{noformat}
{note}
# utils/misc.rb
## Thread.log.data "MISC_STORAGE_SELECTTUBE_TO"
## Thread.log.data "MISC_STORAGE_SELECTTUBE"
## Thread.log.data "MISC_STORAGE_SRCTUBE, tube=" + startingTube.to_s
## Thread.log.data "MISC_SRCTUBE"
## Thread.log.data "MISC_DSTTUBE" 
# utils/sampler.rb
## Thread.log.data "SAMPLER_SAMPLED, " + "volume=%.1f" % sampledVol
# mission/08sep.rb
## Thread.log.data "MISSION_START, esp=#\{ESP::Name\}, mission=#\{ESP::Mission\}, starttube=#\{startTube\}, fromtube=#\{fromTube\}"
## Thread.log.data "MISSION_END, esp=#\{ESP::Name\}, mission=#\{ESP::Mission\}"
{panel}
{note:title=Above was changed}
Essentially the message are the same, but Brent pulled the method calls into a :protocol method defined in utils.rb so the individual protocols don't have to do anything specific.
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<property name="body"><![CDATA[Present:&nbsp; Jim, Wayne, Brent, Cheri, Scott

h3. Machine Builds

* Brent needs radio pieces that he can't find since the WF cruise.&nbsp; Gene may know where they are.
* ESP's are not Wi-Fi capable, but will work only on the boats.&nbsp; Issues with MBARI's firewall make it difficult to use wirelessly here on shore.
* Brent discussed some difficulties we will have trying to modem connect to both ESP's and the vertical profiler's.&nbsp; May require some radio switching from point-to-point to point-to-multipoint.

h3. MFB

* Issues with one of the PCR modules MAY be related to poor heater film connection plug.&nbsp; Chris P will test (with Cheri's help) and if not resolved, we'll switch to another module.
* Build of the final 4 MFB's should be complete by Sept 4.
* Chris P. may need MFB protocol change.

h3. Drifter&nbsp;

* work will not begin on drifter tension control until after McStar is deployed (Sep 29).

h3. Software

* MFB2 hast latest firmware; must still be loaded on MFB3
* Gordon working well with the latest firmware and GUI code, but still needs extensive exercising.

h3. Deep ESP/DWSM

* Pressure transducers are supposed to arrive Monday.
* Scott adding another thermostat to the heater ring which may provide finer control of in-ball temp's
* Brent pushing for gas-infused liquid (i.e., club soda) testing to see how DWSM handles large amt of boil-off.

h3. GUI


h3. Deployment Issues

* Sept 24 triple deployment.&nbsp; Moe at M0, Bruce at Santa Cruz, and Mack in 16m of water only 5-7m deep.&nbsp; Will needto adjust mooring for that one.
* Sep 30 is MARS.&nbsp; Brent has to give talk that evening so may not be on ship unless guaranteed to be back early.

h3. &nbsp;Other Items

* Jim will handle Abe's renewal for using his house for radio access.&nbsp; Same as last year; $599 for 1 year of use of his cable modem setup and for allowing us to mount an antenna on his house.]]></property>
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<property name="body"><![CDATA[Scott ran this meeting.

h3. DWSM

&nbsp; Design review for Elevator&nbsp;&nbsp; - We will be holding an Email PDR followed by a CDR
&nbsp; Sphere status - It is in Oregon at Wah Chang
&nbsp; Construction update - Progressing with ½ of the tubes in,&nbsp; Sample done with rotary actuators.&nbsp; Actuators need calibration
&nbsp; Encoder and Xilinx - Old working code breaks with new Xilinx compiler 10.2.&nbsp; Wayne is going to try using an evaluation license of a different compiler to see if similar results are obtained.
&nbsp;

h3. MFB

&nbsp;&nbsp; Schematic progress - Jose started but was stopped by Brent stating things were going to change.&nbsp; Chris S. noted that the AIV is not placed as it will be when integrated to the core.&nbsp; The AIV needs to be added to the standalone system.&nbsp; We will use existing core harness to make the MFB until we have finalized the shape and location of the MFB.&nbsp; As far as the electrical harness are concerned, the schematics are complete we just need to add lengths to them once they are determined.
&nbsp;&nbsp;&nbsp; MFB needs a written engineering checkout procedure.
&nbsp;&nbsp;&nbsp; Single connector - Was done the above mentioned issue has cause for change.&nbsp; I am trying to move towards a Stand-Alone support box which continues to support the notion of single connector switching.&nbsp; This means that the host, gateway and I2C power supply may be removed from the MFB Grill.
&nbsp;&nbsp;&nbsp; AIV to Grill
&nbsp;&nbsp;&nbsp; ASV air port still is leaking we need to come up with a solution.&nbsp; This port needs to hold at least 200uL and be cleanable as well as vent to a clean air source.
&nbsp;

h3. Software

&nbsp; NEO test run update - the changes seemed to have worked as there were no failures.&nbsp; Memory consumption was down due to restructuring of the Ruby "eval" routine.
&nbsp;
Science - Light puck comparisons between NEO, MaCK and, Bruce; and then figure out why different.
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -
&nbsp; HV puck - ESP needs to resurrect the HV path as a research project.&nbsp; Some issues are: How to seal sides, long term reusability and,&nbsp; what ever else crops up fro this work.
&nbsp;&nbsp; Pucks - In all our puck orders we never order the HV pucks.&nbsp; We need to order some so that we can start this works.&nbsp; This should be done in conjunction with ordering more complete sets from MOE.
&nbsp;
MOE - Temperature calibration done as well as pressure.
&nbsp;
O-rings\- Doug ordered Silicone and Viton O-rings.&nbsp; Viton are 75 durometer which is most likely to hard and Viton does not work well with Ethanol and Methanol.&nbsp; Silicone is not the best for the alcohols but usable.&nbsp; Roman will be immersing the two types into some of the fluids used to check compatibility that way.
&nbsp;
MaCK and Bruce are ready to move
&nbsp;
We need a place to store the Orange Cart as it is not needed to hold an instrument and takes up building b lab space.
&nbsp;
Next build, possible two in the spring.
&nbsp;
Wayne has Hosts in his office, if you need one feel free to take but, do not feel free to not send an email.&nbsp; Please send Wayne and Dick an email letting them know you have removed one and where it will be used so that we may track them.
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<property name="body"><![CDATA[h3. Deployment Update

* Deployment pick-up will be Monday, Oct 27.&nbsp; Roman M., Scott, Jim, w/ divers Kim R, and Lonny.&nbsp; Meet at MBARI @ 5:30am, lv for SC 6:00am.&nbsp; Should be back around 2:00pm.
* Machines/moorings will be unloaded in high-bay.&nbsp; Have permission to store there until Friday until we find final resting places.

h3. Machine Builds

* MOE:&nbsp; BOM will be finished by end of today.
* GG's hand is now in Moe.&nbsp; It's sticking in some positions.&nbsp; Will remove, clean, and lube.&nbsp; If we re-use, we'll use GG's gains...
* After a 3 day 'break-in' period of the problematic harmonic drive, it is now drawing near correct current levels, so we may try to reinstall in Moe.

h3. MFB

* Voltage-regulator boards:&nbsp; Addie needs 9, Cheri needs 3; we are having Jose order parts for 12 Voltage Reg Boards and 15 power boards.&nbsp; Boards will need to be spun but time factor is the same as if we did them in house.
* Wiring schematic of MFB:&nbsp; Addie will make sketch and handoff to Jose/Scott for official ORCAD schematic.
* Serial Cable to PCR module; currently 2 kinds depending on if its a stand-alone MFB (plugging into MFB host) or mounted on core (plugging into Sleepy).&nbsp; Idea will be to make 1 connector that will work in any situation.&nbsp; Addie/Brent/Scott will work on setting this up.
* Brent thinks we could use 4 more 64mb Host boards.&nbsp; Addie will order.

h3. Software

* 10 host boards checked-out, but still need ribbon cables.&nbsp; Addie will order after getting specs from Brent.
* Bufflehead clone is complete and now called Tern (which is Jason's old machine; size about 40GB).&nbsp; Bufflehead will eventually move to Wayne' office.
* running a superphase (BAC and PCR together) shows there are threading issues in the current (old) Ruby.&nbsp; Solutions:
*# &nbsp;Keep fixing this version of Ruby (v1.68), as it's small and has evolved with the current machines
*# Take the most reliable version today (v1.86; working on v1.9), put in our patches and test--could be 3 weeks work.
* Decided to run NEO in debugging mode when it returns and track down the superphase threading problem.&nbsp; If it's always in the same place then we fix and go with solution #1; if it's always in a different place, we discuss solution #2.

h3. DWSM


h5. Sphere pictures in {color:#990066}*/projectlibrary/ESP/DWSM/4k DWSM/4k Sphere Pictures/4k Sphere machining{*}{color}

* Top 1/2 of sphere; was not able to do complete clean-up cutting.&nbsp; Doug will check when it comes off lathe.&nbsp; Bottom 1/2 is now off lathe and on the mill.&nbsp; Both should be ready in 2-3 weeks.
* Doug working specifics of o-rings--could be $15/each.
* Brent suggests we use current dwarves/software because DWSM not ready for full-blown new stuff.
* Addie adding some motor mount pieces to the current machining order that Doug will need.
* Mark Brown notified that we need to get on Port Hueneme schedule.

h3. GUI Development


h3. Other Items:]]></property>
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<property name="body"><![CDATA[Present: Scott, Doug, Chris S., Kevin, Jim, Cheri, Brent, Wayne
Absent:&nbsp; Addie (SolidWorks training)

h3.


h3. Machine Builds

* &nbsp;Scott wants to change power connectors on our 3 surface cans; current ones are starting to break.&nbsp; Total of $4K.&nbsp; Yes, we will do--charging to 900612.
* Moe finished with pressure calibration.&nbsp; Fluid has been moved through the core.&nbsp; All that's left is temperature calibration (cold, room, hot) which should take 2 days.
* {color:#3300ff}We must add '{color}{color:#3300ff}{*}{+}light{+}{*}{color} {color:#3300ff}{*}puck{*}{color} {color:#3300ff}checkout' to our checkout procedure to help understand camera variability.{color}
* {color:#000000}must change O-ring material--cracks discovered on Moe's o-rings, where no fluids have been run.&nbsp; Will go to Viton or Silicon.{color}

h3. MFB

* &nbsp;Writing schematic for MFB is turning out to be more difficult than first thought because of prior documentation.&nbsp; Scott working to fix the mess.
* MFB valve problem that stopped our dye testing yesterday turns out to be a wrong valve assignment.&nbsp; Unclear how assigment got changed, but Scott to track down.
* Jim will talk to Jose about having parts ready for Addie's McLane build.&nbsp; Jose gone the month of December, and we need 2 wiring harnesses, 2 voltage regulators, 1 I2C power board before he leaves.
* Question came up as to how close the grill is for niave user (Kendra) to start pushing fluids and do a basic checkout.&nbsp; Must call Addie.

h3. Software

* &nbsp;Debugging on Neo is running, but so far no problems.&nbsp; It is running all contextual sensors, but one difference with deployment is that is running on the network, not locally.&nbsp; Reason for this was....
* Also, small change to the Ruby interpreter was installed that now releases dead stacks, so it doesn't try to chase any dead references.&nbsp; This may have fixed our problem.
* All NEO software will be merged back in the main trunk, which may cause problems for Bruce and Mack.&nbsp; Since these two are going to be run hard, Brent should check with Chris before this merger takes place.
* Scott has plan for using himself and Wayne to set-up a Dwarf Gateway in early December when Wayne returns from India.

h3. DWSM


h6. +Sphere+

* Spheres are finished at Tapemation (YEAH\!\!), and we will ship back to Wah Chang for dye testing.&nbsp; Dye testing =$500 total.&nbsp; Unknown shipping costs.
* Titanium vs. SS sphere fastners.&nbsp; We discussed; TI=$1800, SS = $200 but will need to be replaced.&nbsp; We will buy TI.
* Min-K's to arrive Dec. 15
* As soon as dye tests finished we will schedule a Port Hueneme pressure test.
* Syntactic foam to arrive by Jan 1-2nd.&nbsp; We will need to send foam out for machining.

h6. +DWSM+

* &nbsp;Sample can is ready for valve actuators and motors+pumps.
* Resample can is still waiting mounting parts, but then just needs tubing bends; pumps already mounted
* 1st week of Dec is when we can start running it.
* Doug wants to purchase some extra motors since we have 0 (zero) extra's currently
* Doug will get r-valve boards and actuator mounts from Addie Monday or Tuesday next week.

h3. GUI Development

* &nbsp;Data import now working in the GUI
* Now it is not necessary to parse through the log files .&nbsp; Still some minor bugs to work through, but Kevin will meet with Brent about this.

h3. Other Items:

* &nbsp;  Scott will run next week's meeting in Jim's absence.
* Scott wants to clean GG of all fluid so he can run a \-5C test with EtOH to check the new 'cold' syringes.&nbsp; Scholin to confer with his team about cleaning GG.&nbsp;
* Will need to purchase 12 sets of batteries for elevator (~$40K)
* &nbsp;WE MUST START THINKING ABOUT ORDERING MORE PUCKS for the NEW MACHINES.
* Ship Schedule: currently working of Revision 1.&nbsp; Much discussion about moving Aug6 day to sometime in April.&nbsp; We will finalize this move next week.
\\
\\ | (!) | *Remember* \\
Please remember to use ESD straps in the bldg A lab, as most of its chairs and countertops have failed ESD testing.&nbsp; Dick Littlefield looking into seat\- |]]></property>
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| 9/6 | 9/7 | 9/8: \\
Gordon into Sphere \\
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| 9/13 | 9/14 \\
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High Pressure Testing | 9/18 \\
High Pressure Testing | 9/19 |
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\\
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<property name="body"><![CDATA[In order for McLane to get access to the source code for the ESP, it was deemed that a CVS server in the DMZ with the source code rsync'd out was probably the best option. The machine prey.mbari.org was deemed as the best fit.  In order to configure prey for this work, the following steps were taken:

# Logged in a root
# ran up2date cvs to install the cvs and received the following:
{noformat}
[root@prey home]# up2date cvs

Fetching Obsoletes list for channel: rhel-ia64-es-4...

Fetching rpm headers...
########################################

Name                                    Version              Rel               Arch
----------------------------------------------------------------------------------------
cvs                                     1.11.17             11.el4              ia64  


Testing package set / solving RPM inter-dependencies...
########################################
cvs-1.11.17-11.el4.ia64.rpm ########################## Done.                   
Preparing              ########################################### [100%]

Installing...
   1:cvs                    ########################################### [100%]
[root@prey home]# 
{noformat}
# Created the home directory for cvs
{noformat}
[root@prey home]# mkdir /home/cvs
{noformat}
# I initialized the cvs home directory using
{noformat}
[root@prey cvs]# cvs -d /home/cvs init
{noformat}
This created the CVSROOT directory and populated it with the necessary files.
# I then created the two cvs related groups using
{noformat}
[root@prey cvs]# groupadd cvsusers
[root@prey cvs]# groupadd cvsadmin
{noformat}
# Created a cvs user (and group) using:
{noformat}
[root@prey cvs]# groupadd cvs
[root@prey cvs]# useradd cvs -g cvs
{noformat}
# Added the CVSROOT environment variable by adding the following to /etc/profile
{noformat}
# Export the CVSROOT directory
CVSROOT=/home/cvs

export CVSROOT
{noformat}
# I set the cvs executable permissions so that it can be run as a service
{noformat}
[root@prey bin]# chmod 2755 /usr/bin/cvs
{noformat}
# Finally, I created the file /etc/xinetd.d/cvs and put the following in that file:
{noformat}
 service cvspserver
 {
         disable            = no
         socket_type    = stream
         wait                = no
         user                = cvs
         group              = cvs
         log_type          = FILE /var/log/cvspserver
         protocol          = tcp
         env                 = '$HOME=/home/cvs'
         bind                = 134.89.2.27
         log_on_failure  += USERID
         port                = 2401
         server             = /usr/bin/cvs
         server_args     = -f --allow-root=/home/cvs pserver
 }
{noformat}
# I then rebooted prey]]></property>
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<property name="body"><![CDATA[h1. Discussion of 18 Feb 2010

Luke Coletti, Doug Pargett, Jim Birch
# &nbsp;For July, 2010 WF cruise, ESP team will use Johnson lab 1Km housing.&nbsp; There were some issues with the last time it was used; weird readings--discussion ensued as to why readings not normal.
# Doug to draw up plans for pressure housing based on original aluminum design, keeping original diameter, using 2 radial o-rings to seal end caps.
# Doug will draw up plans for probe head opening using the actual probe he has, and getting rid of the current goofy SAE opening.
# We will make 2 Ti housings; ESP pays for 1, Johnson lab pays for 1.
# Eventually we will power the deep ISUS from our Deep-Sea Power and light battery stack, which will allow recharging if needed.&nbsp; But for July we'll use Luke's battery pack (especially since it's such a short deployment).
\\

h1. ISUS specs

&nbsp;Based on Luke's LOBO experiences, one 'single stick' battery pack will power ISUS for 6 months if sampling once/hr.&nbsp; Thus, 20 min sampling rate would last \~1.2 months.&nbsp; Duration scales proportionally.
\\
\\
\\

h1.


h1. Continued Discussion 31 August 2010

Luke, Doug, Scott, Jim, Ken
\\

1.&nbsp; How will we power ISUS on DESP?&nbsp; ISUS runs on 8-20V, 6-7 watts nominal.&nbsp; Current plan is to run off the DESP batteries.

2.&nbsp; Ken said they can build 2 ISUS starting right now.&nbsp; One will be shallow, one deep.&nbsp; We have also asked for 3 deep probes ($2200/ea).

3.&nbsp; Luke will give Doug plans to modify the calibrator, and new flow-cell for calibrations; these are nec with the new titanium housing design.

4.&nbsp; Doug will send [plans|^4000mISUShousing.pdf] for Ti housing out for bid.&nbsp; Next steps will be determined by cost/time estimates.&nbsp; Ken has offered us his aluminum housings for deep work.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Scott, Bill, Kevin, Brent, Chris P, Chris S., Doug, Jim

h3. JdF Preparations


h4. Wand

* Doug's selected a tubing (150F limit and metal reinforced) that looks promising.&nbsp; 30' necessary; may need to heat it to get curl out.
* Pumps and fittings are here.
* Need to check with Pete on whether Ti screen is necessary, or is SS okay?
* Brent leaving June 9 - July 6.&nbsp; Must do much rejiggering
h4. DWSM
* New encoder is in and has depressurized from 3100psi (but did have 900W peak\!)
* Sample bags still has broken switches
* Resample side needs hydraulic damper added
h4. Other
* ISUS.&nbsp; Will check with Luke on where the development of Deep ISUS is.&nbsp; Must be tuned to sulfides.
* ISMS.&nbsp; Must have it before tank testing.
h4. Dates

&nbsp;April 25 \-\- First build of DWSM and wand test.&nbsp; Probes from Pete should be ready for printing.

April 27 \-\- Roman returns from WHOI

May 2 \-\- Core testing begins.&nbsp; Sphere Electronics are in.

May 9 \-\- Second DWSM build

May 16 \-\- Gordon Ready?

May 27 \-\- Gordon must be in ball&nbsp; (this likely to move FORWARD, as we'll be ready sooner)

June 20 \-\- In test tank

h3. Software

* GUI.&nbsp; Would be good to get Stanford folks access to GUI and link shore-station data to our external FTP-site.
* Kevin to look into getting I.S. to r-sync to shore station and deal with this.

h3. WHOI Deployment

* Bruce has made it\!\!
* Reminded that we should try and get acceleration data on our moorings in this area of fast tides.
* Scott got Andy's accelerometers (pieces) and will build two...&nbsp;
* We must still press WHOI to mount CTD on ESP-Chris so we know what's going on down at the can.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Scott, Bill, Chris S., Jim, Elif


h3. JdF Preparations/ASTEP II Issues



h4. DWSM

* Ti housing discussion.&nbsp; Doug sent note outlining where he thought this issue fell on the importance scale.&nbsp; Although a year-long deployment was promised in ASTEP II, it may be so cost-prohibitive (due to many other things besides the DWSM bell-housings), that we fall-back to shorter deployments.&nbsp; Must talk to Doug more about this and perhaps get other opinions on experience with long-term operations.
* Temperature Sensor on Wand.&nbsp; Bill thinks it has a very linear response and decision is to wait until Doug returns and has more wand completed before end-to-end testing of the temp sensor.
* Just on track for an April 25 DWSM build.&nbsp; Doug has assembled many of the parts nec for testing bag/switch subassemblies before rebuilding.
* Teresa working on shipping dates/logistics; our contact with this is Bill U.

h4.


h3. WHOI Deployment

* Scott has accelerometer working; It will record Accel at 10hz for \~9min then spend \~1min writing results to flash.&nbsp; Much thanks to Scott for the 1-wk turnaround, getting the job last Thursday and completing the build/checkout by today.
* Scott leaves Saturday and will be gone tomorrow (Friday) for packing.
* Some discussion about the wrong o-ring groove in the clamps of ESP-Chris.&nbsp; Why? Is it a drawing or manufacturing issue?&nbsp; Scott tasked with checking this out, and providing info to WHOI on how they should proceed.&nbsp; Do we fix ESP-Chris, or is there chance we will be flipping ESP-Bruce to do another 45 days?

h3. G3

* We have contracted Airflow Sciences to perform CFD analysis on a 10.5' LRAUV vehicle with enough data for Rob M. to calculate stability and fin area's for this larger vehicle.&nbsp; Should have results in \~2 weeks.&nbsp;&nbsp; This would give us a 3' payload space if the increased drag of a longer vehicle is acceptable to LRAUV team.

h3. ESP Drifter

* Cruise is Sept 6-21.&nbsp; Phone conference immediately following this meeting with Matt Church and group at UH to discuss preliminaries of the cruise.&nbsp; Gene handling logistics once we get instrument to HI.&nbsp; Teresa has given Jim some container/van info for the transit across the Pacific.&nbsp;
* Brent working on Drifter comms.
* Discussion initiated by Scott that, with the addition of adaptive sampling code, we need (even more) to cordon-off ESP brains from mooring control.&nbsp; Perhaps the board Brent is working on as a mooring controller for Drifter could become the ESP standard, taking over adaptive sampling chores as well as contextual sensor coordination, while leaving the ESP to do only one thing.&nbsp; This idea is gaining traction; we will look into what other mooring controllers have been developed at MBARI, and/or if there are other S.E. to help with this to not put another log on Brent.]]></property>
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<property name="body"><![CDATA[h5. Background

In order to really interact with the ESP, it was clear that some level of Ruby integration would really be best in the GUI.  For this reason, I turned to JRuby in order to be able to access a Ruby engine from within the GUI.  I used the information here:

http://kenai.com/projects/jruby/pages/RedBridge

to get me going.  I chose the Embed Core way of doing it as I thought it would be the best way to do what we need to do.

h5. The Ruby environment

In order to understand much about the scripts, the Ruby interpreter uses several environment variables to figure out what context and configuration the ESP is running in.  Those variables are:

# *ESPhome* - is the top level (root) directory of the ESP source code tree.  
# *ESPname* - is the name of the ESP machine. Note this may be the hostname of the machine that it is running on, minus any "esp" that is prefix removed.
# *ESPmode* - is the operating mode in which to run the ESP software
# *ESPlog* - is the root directory under which all data files are written
# *ESPpath* - is a list of directory to search for mission scripts
# *ESPconfigPath* - is a list of directories to search for configuration files

In the GUI, it can interface with one or more ESP, so basically, these variables should be stored with the instrument information. The strange thing about this is that they will only be applicable on the machine where the ESP software is running, which is NOT where the GUI will be running.  The reason to have this information in the GUI however is that at some point the GUI will have to get access to the same source code tree and so even though the ESPhome and ESPlog variables will be different, everything else will be relative to those root directories.  Here is a logical deployment of the ESP network and a GUI client.

{gliffy:name=GUI ESP Deployment|space=ESPAPP|page=Ruby integration|pageid=11239895|align=left|size=L}

h5. Interactions

All of the ruby code for interacting with the ESP is located in MBARI's CVS system.  In order to reference the ruby scripts, they need to be in the classpath for JRuby.  I thought the best way was to have the user point to the head of the directory tree and then basically have the GUI crawl that and build the JRuby classpath dynamically.

The scripts that were active during the ESP's run will be co-located on the FTP server where the logs and images are stored.  They will be in a folder called esp2local.  So when a user is interested in synchronizing the GUI application with the current files on the shore based FTP station, it should create a local copy of all the files on the FTP directory so that it has a local place to get to the ruby scripts.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Bill, Brent, Jim, Doug

h3. Discussion Items:

* Airflow sciences has been given the PO to perform calculations on a 10.5' vehicle.&nbsp; They are working on it now.&nbsp; Results in \~1 week (?) .
* Note sent to Tong Chen of Teledyne describing high-level needs for sampler component to see if they might be interested in collaborating.&nbsp; He forwarded to Mike Metcalf and 'others'.

h4. DWSM

* Doug testing a new bag cap assembly.&nbsp; This led to a lengthy tutorial on the construction of the bag cap and the problems he's seeing with the pressure compensation component.&nbsp; Now we know what the problem is (too much oil in the compensation-side of the system), such that the bag-empty switch is not thrown.&nbsp; Switches always seem fine; it's the hydraulic line that is&nbsp; leaking.&nbsp; Unclear why/how this leakage is occurring.
* Still on track for a first build of DWSM on Monday, April 25.
* Doug has wand designed; parts going into shop soon.&nbsp; Will work with Scott to have complete electrical build of the wand system finished next week for testing.

h4. {gliffy:name=wand plumping\|space=ESPAPP\|page=Apr 21\|pageid=16777299\|align=left\|size=L}


h4. ESP Drifter

* Brent has been wrestling with his choice of host board.&nbsp; Finally can write files to internal flash, but must turn off lots of bells and whistles, making board much slower.&nbsp; Now will start layering things onto this board.&nbsp;
* Moxa boards work with the x86 but unclear if it works on embedded host.&nbsp; This is next hurdle.
* Will meet with Gene and Doug Monday to discuss Gene's battery tube needs.&nbsp; Might be some issues with the size he needs.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris S., Elif, Jim, Bill, Chris P.

h3. &nbsp;Items

* &nbsp;Reviewed schedule.&nbsp; Chris P. think we are on track, although large amount of work looming.
* Harvard never responded to my request to join us.&nbsp; We expect probes from them this week.&nbsp; They are working frantically to get things to us on our timeline.
* Still deciding what to put on mRNA arrays; should know by Friday this week.

h4. CANON

* &nbsp;Nitrate is incredibly low right now, so we will force-fire the full phase so the WCR can be ready when things become interesting.&nbsp; Prediction is that nitrate will start coming up later in this week.&nbsp; Should start blowing this PM.&nbsp; Trigger's now set for 9umole, then 15 umole.&nbsp; We hope to better coordinate with LRAUV on Thursday/Friday for front following.

h4. Reagent Progress

* Bill has been testing ethanol in the diluent (?) to keep crystals from forming.&nbsp; Looks like we get a little over a two cycle shift in Ct's (worse) than Qiagen.&nbsp; We will not be using ethanol.]]></property>
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<property name="body"><![CDATA[Present: Julie, Chris P., Roman, Bill, Jim, Chris S.
\\
\\

{color:#0033ff}1. &nbsp;PCR paper layout. &nbsp;Chris S. will present outline, fig ideas, holes. &nbsp;Discuss which journal to focus it towards.{color}
* Chris started the layout and many decisions still need to be made about how many machines to include in building standard curves, and which deployments.&nbsp; Discussion ensued.&nbsp;
* She will have Figure ideas next Tuesday.
\\

{color:#0000ff}2. &nbsp;M0 leapfrog deployment. &nbsp;Julie, discuss your plan; what are Chris P's, responsibilities in this?{color}
* We need to use only 1 probe set from beginning to end of deployment. MaryAnn from U. Ga, wanted liquid back but that ain't happening.&nbsp; We are still trying to decide which P/P set to use.
* Moe goes out April 15 on Zephyr
* 30 days later, Neo will be flipped for Moe.
\\

{color:#0000ff}3. &nbsp;Do we need new targets for Nov MARS deployment of D-ESP. &nbsp;If yes, must develop libraries?{color}
* {color:#cc0000}Tabled{color}

{color:#0000ff}4. &nbsp;Progress on '08/'09 paper. (John returns 2-12){color}
* {color:#cc0000}Tabled{color}

{color:#0033ff}5. &nbsp;&nbsp;ASLO practice talks. &nbsp;I've reserved Pacific Forum Friday, Feb 19 10am-12.{color}
* Everyone is happy and excited to get their talks done the week before and practice them.

{color:#0000ff}&nbsp;{color}{color:#0000ff}6.&nbsp; Gordon Results{color}
* &nbsp;{color:#cc0000}Tabled{color}

{color:#0000ff}7.&nbsp; New IPC results{color}?
* We will order 10K rxns from Sandy. (or Melancon if he can deal with large number and has approval to be a reagent reseller from ABI)
\\

{color:#0000ff}8.&nbsp; Pete & Vik groups schedule. And are they taking instruments back??{color}\\
* They arrive Monday (MBARI Holiday) but have Chris P phone number.
* Vik bringing 5 p/p sets and will use MFB #9
* Pete's group will bring 1 Cyber, 1TAQ assay, will use MFB #2
* Reasonable target to ship them their MFB's is March, 2010 (Vik first, then Pete's group)
\\

{color:#0000ff}9.&nbsp; MOE script upgrade after Julies MOCK deployment? Should new IPC be included on the MOCK??{color}
* Cold testing will begin this week with Moe.&nbsp; Engineering is standing by to help Julie can the instrument.
* Julie will upgrade scripts after the cold test, but before the deployment.
* I don't remember what we decided about including new IPC into the mock deployment

{color:#0000ff}10.{color}{color:#0000ff}&nbsp;{color} {color:#0000ff}DA testing{color}
* We will begin Bruce DA testing next so Roman can watch it.&nbsp; He's working with Bruce K. now and training is going slowly because there is so much to learn.&nbsp; We will be sending Roman out to WHOI to help with acceptance testing.

{color:#0000ff}11.{color}{color:#0000ff}&nbsp;{color} {color:#0000ff}S. California deployment{color}
* Chris S. working on boat issues, looking like we may use Shanna Rae, but haven't heard from Christmann.&nbsp; S. Cal will put two moorings in San Pedro Bay and run Hab/DA/WCR.&nbsp;
* We need to simply set a date and go there, as the guys down south don't know what to tell us on dates.

h1. Various

* We need to begin a list of how to test extraction and archiving protocols that would work the best.&nbsp; This will get more complicated as other&nbsp; groups start adopting our work.]]></property>
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<property name="body"><![CDATA[Chris found this valve ...
[http://www.parker.com/literature/Literature%20Files/Precision%20Fluidics%20Division/UpdatedFiles/PACE%20Data%20Sheet.pdf]

These valves used by Kia Peyvan of Custom Array:

(from 9-7-2010 email)


BTW, Jim the company with the tiny valves is called Takasago.&nbsp; I use their KV series (http://www.takasago-elec.co.jp/cgi-bin/en/index03.html) .&nbsp; If you have a very small space you operation in they are good.&nbsp; But burkert valves are still the top of the line in my opinion.

&nbsp;]]></property>
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<property name="body"><![CDATA[Present: Julie, Chris P., Bill, Jim, Chris S. John

Absent: Roman\\

{color:#0033ff}1. &nbsp;PCR paper figures.&nbsp;{color}

* here is tenatative plan:# Fluidic path of MFB and abridged core diagram
# image of bkgrnd subtracted triplicated standard curve
# table \--avg PCR effect
# Lab triple PCR graph
# M0 climatology data
# panel graph of field data and array examles
# AUV data (?)
# 3-d plot of nitrate/temp/salinity vs. abundance&nbsp;&nbsp; \-or-&nbsp; time resolved---3 time plots* Chris will have rough figures at our March 9 meeting.

{color:#0000ff}2.&nbsp; IPC order through Spyglass?{color}
* We will be getting 5000 reactions, (which is 10K for us since we use it at 1/2 dilution), which will be enough to get us through the spring/summer deployments.

{color:#0000ff}3.&nbsp; Precruise for March deployment?{color}
* Charlie will do this.&nbsp; We must do the July one, using same missions as March so pilots know what equipment we want.

{color:#0000ff}4. &nbsp;Progress on '08/'09 paper.{color}
* John just got back and will be working with Roman on keeping paper moving forward.&nbsp; he wants to turn '08 data into cell-counts.&nbsp; May use Diane for this but will first check with Roman to see what his bandwidth looks like.

{color:#0033ff}5. &nbsp;&nbsp;ASLO practice talks.&nbsp; Friday, Feb 19 10:30am-12.{color}
* Moved time back 1/2 hour to accomodate Chris S.

{color:#0000ff}&nbsp;6.&nbsp; Pete & Vik groups schedule. And are they taking instruments back??{color}\\

Groups getting trained; Pete sent 2 grad students who just want to drive the ESP.&nbsp; Plus a student from Zehr lab, plus Orphan's people.&nbsp; First reactions did not work--might be the master mix.
{color:#0000ff}7.{color}{color:#0000ff}&nbsp;{color} {color:#0000ff}DA testing{color}
* Roman has not been seen to ask what the status of this was.&nbsp; He was busy training Bruce Keafer last week, no no DA testing yet.

{color:#0000ff}8.{color}{color:#0000ff}&nbsp;{color} {color:#0000ff}S. California deployment{color}
* Chris S. working on boat issues.&nbsp; We have prices from Christmann, but need to see what Scott's found.&nbsp; Will finialize by middle of next week.
* New E/M cables are in the qeue so we can deploy at 12-15m depth.]]></property>
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<property name="body"><![CDATA[h3. Items

1.&nbsp; Discussion of Cawthron visit (Chris Cornelisen and Rowan Strickland).&nbsp; Looking at a Feb, 2012 deployment.&nbsp; Discussion of potentially sending 2 machines.

2.&nbsp; Discussion of upcoming schedule after JdF.&nbsp; The fall may see a pier deployment at SC wharf.&nbsp; M0 deployment unclear; unsure of CANON intentions in the fall.* idea to not go on MARS until April 2012 and stay until October.&nbsp; This would permit extensive exercising of adaptive sampling, some preliminary discussion of how we'd trigger...
3.&nbsp; Teledyne contract/collaboration
* What 'item' is confined/defined enough that we could use them to help?
** pizza-pie concept
** sampler filter elements.&nbsp; How contained?&nbsp; What is filter size?&nbsp; Pursue tangential filtering, or give them requirements and that as a possible solution.
** Boards are also well-defined, but we may be going to different actuators, so boards may be very different than what we are currently using.
* Jim talking to Metcalf tomorrow (Friday morning).&nbsp; {color:#ff0000}Update{color}:&nbsp; He had lost all his notes from our March 10 meeting (misplaced his iPad), and couldn't really remember what we had wanted.&nbsp; I reminded him of the email and (some of) it came back.&nbsp; He said he'd farm ideas around and would like to meet again, by early June. sigh.

4.&nbsp; Will contact McLane about our HV pucks.

5.&nbsp; Need to have a 'lessons-learned' with Yanwu regarding adaptive sampling, given our recent CANON experience with event triggering.


h3. D-ESP

1. &nbsp; This past week was the 2-year anniversary of the first deployment of the sphere and elevator.&nbsp; There was a party and much frivolity to look back and see how far we'd come.

2.&nbsp; DWSM bag switch problem
* Doug thinks he's found how oil is creeping into the hydraulic system rendering the bag switches inoperable.&nbsp; Leakage around barb fittings.&nbsp; Will try permanent glue at all fittings.
* 1st build of DWSM is ongoing.&nbsp; Sample side progressing well with pulse suppressors in, and IEP replacement motor in.

3.&nbsp; Harvard having trouble lysing their thermophiles using our reagents/protocols.&nbsp; Pete suggesting maybe putting other assays on the MFB, but little time to develop new probes/primers.&nbsp; Older, proven probes/primers will give little scientifically interesting data.&nbsp; Looks like JdF may be turning more into an engineering test and archival mission.

4.&nbsp; Chris preston having trouble with lysing thermophiles for SHA; will try bead-beating just to see if the arrays work. ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Kevin, Chris P, Roman, Chris S, Elif, Jim, Bill

h3. Items:


h4. WHOI deployment

* Kevin returned from a GUI-development week, where he rec'd much positive feedback on ESP GUI.&nbsp; Many changes have been implemented.&nbsp; New version should be on Confluence by Friday.&nbsp; Older versions will then not work, as database structure has&nbsp; been changed.
* Complicated plans for ESP-Bruce recovery, depending on contingencies.&nbsp; Roman leaving May 21, to return June 11, unless he needs more time to run standards.&nbsp; This necessary as ESP-Bruce is giving very low numbers of _Alexandrium_\--more investigation needed as to why.&nbsp; Final plans will solidify as June 7 approaches.
* {color:#ff0000}ACTION ITEM{color}\-\- Chris S. to contact WHOI to have a final conference call discussing this swap on June 7 and the various contingencies.

h4. JdF

* &nbsp;Mission and communications to D-ESP will be unique.&nbsp; Unlikely we will need GUI for this cruise.
* Currently in the middle of qualifying 6 p/p sets for qPCR.&nbsp; Have learned that Harvard never ran any of these on an MFB, and some were only minimally characterized on their bench-top instrument.&nbsp; Standards for their two methanogen p/p were either bad, or not here yet.&nbsp; We aren't in trouble, but there is not much time-margin left...
* Roman printed SHA arrays yesterday, but didn't like the print quality.&nbsp; Too much power and not enough hydrophobic tip coating caused 'splash'.&nbsp; He's re-doing them today.
* Logistics still need working out:
** crew list and bunk space
** Flatbed will leave MBARI on July 6, arriving for unload in Newport on July 8.&nbsp; Instrument loaded on ship on Monday, July 11.&nbsp; Shove off July 12.&nbsp; Will discuss travel to/from Newport at engineering meeting.
** Screen on end of wand.&nbsp; Doug P suggests a 0.2mm screen size from Ti.&nbsp; Can't find a 0.5mm one in Ti.&nbsp; Do we have contingencies if it plugs?&nbsp; No.&nbsp; Maybe make it big and bulbous to lessen the likelihood of plugging.

h4. Other Items

* We will buy the 'suck-and-sniff' He leak detector.&nbsp; put on 900915.&nbsp; Roman will order.&nbsp;
* We will by optode for O2 sensing for D-ESP (see Feb 15 notes).&nbsp; Still needs ordering.&nbsp; Roman.
* The Fall deployment schedule still somewhat unknown.&nbsp; We will be putting an instrument on the pier, but unknown exactly when.&nbsp; Will an instrument be in the bay at/near that time?&nbsp; Still to be determined.&nbsp; There would likely be the first time(s) the new GUI would really be put through its paces.
* Bill and Chris have been testing whether EtOH would be a better diluent then our current SPEdil, but notice a 2 Ct shift (worse) with EtOH.
* Chris P talked of doing direct PCR on 0.2 HA filters to look for viruses.]]></property>
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<property name="body"><![CDATA[After a busy start to 2010, I am just getting my head back in to the ESP development.]]></property>
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<property name="body"><![CDATA[Present:  Brent, Scott, Chris S., Chris P., Bill, Jim, Doug

h2. Items:


h4. JdF Preparations

* Many decisions made on logistics of JdF cruise:
** Shipping van will be kept at 15C for both shipping up there and returning.
** Wireless network will already be set-up before shipping, so Chris P. can run the dock test whenever convenient before the 11th.
** Chris P. to be in Newport on July 8 when Van arrives.&nbsp; Engineers will arrive on 9th or 10th.&nbsp; Load ship on 11th.&nbsp; Shove off July 12.
** On return, planning for ship unload on July 23.&nbsp; Engineers can leave July 24.&nbsp; Bill to see to van loading and see it off on July 25.
* &nbsp;IEP pump needs calibrating after new pulse dampeners installed.&nbsp; Brent and Doug looking into that.
* Gordon does not need to be in ball before May 27, as originally planned.

h4. Hawaii Drifter preparations

* &nbsp;We recalculated numbers for the power budget, which showed how difficult the mission planning will be for the drifter cruise.&nbsp; Chris S. will talk to Zehr/DeLong about their needs and how many samples/ how much water they will want to collect.
* Chris would like to be able to 'check-in' to the Drifter from MBARI.&nbsp; Brent says that is very likely; will work on when he returns from Europe.

\\]]></property>
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<property name="body"><![CDATA[Still getting up to speed on where I was at.  I used Enterprise Architect to reverse engineer the Java code for the whole GUI part of the project as well as created a nice Data Model from the database on Fog.  VERY NICE!

It is clear through discussions with ESP team and such that I am not sure I am going to be able to get around the Ruby integration with they way things need to go.  For this reason, I am refreshing my view of JRuby.  The nice part about this, is I might be able to automate some of the things that users had to do before (like create phase and protocol descriptions).  It will also help in dealing with instrument state as well as parsing the log file.]]></property>
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!core model.jpg|thumbnail,align=left!]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris S., Chris P., Bill, Julie, Elif, Jim, Roman

h2. Items


h4. &nbsp;ESP Drifter and Hawaii Cruise

* &nbsp;Chris/Julie's preliminary work shows that waste volume allows only 40 assays.&nbsp; Thought is to perform 40 WCR's and 17 PCR's.
** We could change {color:#cc3366}MFB Final Purges{color} to {color:#3300ff}Final Purges{color} to save on waste space.
** Want 2L volume for each sample.&nbsp; Need to know how long for power-budget calculations.
** Julie to test both the above issues,
* Plan is to do DeLong's stuff first (2-3 days of WCR every 2 hours), and intersperse the PCR within that.&nbsp; DeLong may lose 2-3 WCR's with this scheme.
* Chris S. suggests dropping it near a front so it will eventually cross.
* Julie has filters from the latest ALoha cruise.&nbsp; She'll use these to create lysate and see how well her p/p work.
* Using MOE for this deployment.&nbsp; Currently, CS is rusted, and waste container seems to be leaking.&nbsp; Roman to work on before leaving Saturday.
* Schedule:
** Cruise is Sep 6-21.
** Will need 1 week prior to MOB to run dockside standards.
** Will ship instrument in refrigerated van, reagents loaded and closed, but not final seal.
** Ship on ~ Aug 19, depending on transit time.

h4. Array printer

* &nbsp;alignment still needed.&nbsp; Hopefully finished by PM today.&nbsp; Will print tomorrow.&nbsp; Chris says she doesn't need arrays, but current print needs testing to make sure.&nbsp; Roman operating as if more are needed.

h4. JdF

* Chris P. and Bill have put much work into a straw man schedule. It is HERE.
* We will not purchase an optode and refit our Seabird CTD.&nbsp; Too much $$. ($5K for optode, $3K to Seabird for firmware changes, plus cables)
* Do we use the Clark?&nbsp; TBD.&nbsp; Must check with company about H2S effects on electrode.&nbsp; Are effects reversible?&nbsp; Bill looking into.

h4.


h4. HAB PCR

* Elif working on getting probes for SHA bugs. ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Bill, Chris S., Brent, Mike Conway, Doug, Chris P., Scott, Jim

h2. Items


h3. &nbsp;JdF

* &nbsp;Discussion of shipping needs.&nbsp; Mike Conway needs to know what is being trucked, what will be on boat, in order to know what Clague can bring.&nbsp; We have no idea what Harvard will want to load.&nbsp; This item needs attention.&nbsp; MBARI will need one complete 48' trailer.&nbsp; Here's the [Santa Moncia shipment|^Shipping to Santa Monica.JPG] for the Methane mound deployment.
* We will have 4 Ro-Pak's, two inside our van and two outside.
* Battery sleds were going in moon pool, but now may be shipped up on this truck (scattered among our van and ro-paks) and disassembled/reassembled in moon-pool area in Oregon.

h5. Mission planning

* Brent already has code that will stop DWSM from starting the next sample if voltage below a threshold limit. This can easily be modified to stop ISMS if voltage drops below a (higher) threshold, in order to conserve power for Core functions.
* Will try to setup a test of this before he leaves.&nbsp; Chris P., to work on mission next week.
* Talk to pilots about mission planning.&nbsp; How does diving each morning to replace battery impact Clague dive plans?&nbsp; What is the radius they are willing to travel from ESP site, as coming up and moving boat will not allow enough time for meaningful work to be done by him at another site.

h5. Communication

* We plan on using same hull transducer in WF for acoustic comms to the D-ESP.&nbsp; Hans Thomas has connectors that allow our Benthos box to connect.&nbsp; Need to check with him about this as date approaches.

h3. Hawaii/New Zealand

* &nbsp;Shipping container being researched by Grech.&nbsp; Must make sure that plywood interior walls do not encroach on the 45"x48" dimensions of Ro-Pak.
* Our goal is a van that can be used 'intermodally' (ship, truck, train(?)), maintain 40-60F, and use available power without too much hassle to convert...
* &nbsp;]]></property>
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OS
Ruby
Protocol
Firmware]]></property>
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<property name="body"><![CDATA[Software Revision level for Instrument NEO
OS
Ruby
Protocol
Firmware

Email from Brent 19 march 2010
Updated Linux OS  (v1.8p2)
Updated Sleepy Gateway firmware  (v3.01) Old, but working, Dwarf firmware (v2.59)
   with special 64hz version for the mfb Latest ruby interpreter  (1.6.8-mbari8B) Old Ruby scripts
]]></property>
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<property name="body"><![CDATA[Software Revision level for Instrument Moe
OS
Ruby
Protocol
Firmware

Email from Brent 19 march 2010
Very old Linux OS  (v1.5)  *** this must be updated  *** Old, but OK, Sleepy Gateway firmware
    (lacks support for DWSM and external sampler)

Old, but working, Dwarf firmware (v2.59)
   with special 64hz version for the mfb

Older ruby interpreter  (1.6.8-mbari7)
Very old, tweaked ruby scripts (some updates not in CVS?)]]></property>
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OS
Ruby
Protocol
Firmware]]></property>
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OS
Ruby
Protocol
Firmware]]></property>
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<property name="body"><![CDATA[These pages are out-of-date (Nov 2, 2011).

Please note when you make changes.


[Betty|ESPAPP:Betty|Software Revision Level of Betty]
[Bruce|ESPAPP:Bruce|Software Revision Level of Bruce]
[Moe|ESPAPP:Moe|Software Revision Level of Moe]
[Gordon|ESPAPP:Gordon|Software Revision Level of Gordon]
[NEO|ESPAPP:NEO|Software Revision Level of NEO]
[MaCK|ESPAPP:MaCK|Software Revision Level of MaCK]]]></property>
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<property name="body"><![CDATA[&nbsp;Present:&nbsp; Jim, Roman, Chris P, Bill
Absent:&nbsp; Chris S., Julie, John

h1. Papers


h4. &nbsp;John & Roman

* John will combine Sept '07 and Oct '08 data.&nbsp; Currently combing through AUV, DA, and HAB data.&nbsp; Chris P. says all physical data for these deployments is in SigmaPlot and she can show Roman how to access.
* After Betty is up and running, and Bruce Keafer is gone, Roman can hit this full-time.

h4.


h4. Chris P./ PCR paper

* Currently picking data out of notebooks, mainly the NEO m0 deployment of May '09 (Nov '08 pulled reagent from wrong valve; data suspect)
* {color:#cc0000}Next week{color}:&nbsp; skeleton outline/figure ideas/holes to fill/which journal.
* Chris sent out her summary of the water quality monitoring work in a Jan 17, 2010 email.

h1. Lab Issues

* Chris reading PICARD manual (new PCR machine).&nbsp; waiting for a loaner PC from Zorba who is on vacation.
* Bruce K. arrives Monday
** Roman will show him how to run ESP--will use Bruce/Mack
** Shannon Johnson will also shadow
** Roman needs Cheri to clear Bruce for operation (done 2-4-2010)

* Bruce has had software rolled back to Oct '08 and will rerun the DA assays; should be finished by Tuesday
* Cheri to look into a light-proof curtain wrap around Bruce so we don't miss pictures.&nbsp; Maybe check with Haddock lab on how to do this.
* Next week Girguis sending two grad students and Victoria Orphan sending 1 tech to learn how to run MFB.

h5. Betty

* has a full carousel
* will start mission on Weds
* over weekend it will sleep, then hammer next week (30 min break b/w runs)
* If it fails, we note detailed documentation on how we recover.&nbsp; Cheri needed here.
* Then +SCIENCE CHECKOUT+; Cheri needs to shadow to learn this for the McLane build checkout.
*** bag reagents
*** load them
*** run tests (projected to take 3 days)
***# make lysate
***# make an array
***# run a phase&nbsp;
* need cell cultures to do this properly; McLane does not have.&nbsp; Might have to work with Bruce at WHOI.

h5. Moe

* &nbsp;waiting for Julie to get back

h4. Gordon

* &nbsp;Looks like PCR reagents are fine when running standards.&nbsp; 1 m/m line had bubble; IPC primer was also pulling funny.&nbsp; Chris found inhibition from normal samples, though.
* &nbsp;
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<property name="body"><![CDATA[Software Revision level for Instrument Betty
OS
 1 March 2010 Version 1.8 by Brent
Ruby
Protocol
Sleepy Firmware
  Sleepy:  3.01
Sleepy CPLD
Core Firmware
  Dwarf:  3.68
Core CPLD
RValve CPLD]]></property>
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<property name="body"><![CDATA[h1. D-ESP


h5. DWSM

* Doug opened sample can and all switches work just fine :-( &nbsp; Much discussion about what to do now.&nbsp; Doug wants to re-build bag assembly, but uncertain how that would help identify the problem.&nbsp; Difficult to know the path forward.&nbsp; Brent/Scott/Doug to meet and discuss.
* Doug's found new sphere Bulkhead valves ($80/ea) and will order 4-5 to replace current (leaky) ones.
* ROV pilots and Craig Dawe working on a dead vehicle recovery option so they could get ROV back if attached to D-ESP while it's hooked to MARS and the ROV dies.
* Doug has no information on the Mass Spec housing (see below)
* Drop weight release neeeded modifications:&nbsp; design now almost finished, then to machine shop.

h5. Mass Spectrometer

* we are experiencing scope creep.&nbsp; Were supposed to receive a turn-key system to mount on elevator, and what Wayne has rec'd still needs wiring work and power supply filters, and currently will not turn on.&nbsp; Also Doug has no specs on the housing
* Jim will set-up another phone conference with Pete to address these issues

h1. Surface ESP's

* Bruce has been turned back to 2008--firmware and Ruby scripts.&nbsp; Some temperature calibrations were out of wack; Cheri did a quick room/hot temp calibration, so those numbers have changed, but everything else is the same.&nbsp; Ready for Roman to start running DA arrays.
* Mack has latest firmware and is running off the networked (not internal) code.
* Betty needs new Linux OS and Ruby Interpreter;&nbsp; for it's month long test run, should NOT run off network as it will hang each time the network goes down.
* All machines need the latest software components (Gordon is only one with all of these)
** Dwarf Firmware (update to 3.68)
** Ruby Script updates
** Linux OS update (from 1.6 to 1.8)
** Ruby interpreter update to 1.6.8-mbari8B
* Brent will work with Cheri to start this process and then hand-off so she may finish the upgrades on all machines.
* Scott will create _{+}machine-specific pages{+}_ in JIRA bug tracker to follow the software version numbers on each machine.

* Brent sent this email 2-3-2010:
{quote}
There's a bit of an ESP configuration conundrum we should discuss.I have had logic in each machine's configuration.rb file that automatically configures out MFB support AND the core's AIV rotary valve if it has no MFB dwarf installed as determined by probing for the MFB dwarf on the I2C bus.
\\
The intent was to allow the cores to automatically recognize the presence (or absence) of an MFB and adapt their configs appropriately.&nbsp; But, this approach is proving not to work well for two reasons:
\\
1)&nbsp; If the MFB is removed from an ESP, it is no longer possible to rotate its
&nbsp;&nbsp;&nbsp;&nbsp; AIV valve (which is controlled by the collection dwarf) because it assumed
&nbsp;&nbsp;&nbsp;&nbsp; to be always associated with an MFB.
\\
2)&nbsp; In simulation, all dwarves appear to be installed.&nbsp; So, ESPs
&nbsp;&nbsp;&nbsp; always simulate as if MFBs are installed.
\\
I'm considering ditching this automatic probing for the MFB dwarf and requiring
that each machine's configure.rb be modified explicitly to exclude the AIV and to
include MFB support as needed.
{quote}
Decision was to {color:#ff0000}remove{color} the auto-detect feature.

* Brent, Kevin, Jim, and Todd Ruston will meet to discuss setting up a CVS account for McLane to get the latest Ruby code.

h2.]]></property>
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# Project overview

h4.

\\
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<property name="body"><![CDATA[h1. Plans


h3. &nbsp;S. California network deployment

&nbsp;Chris still pinging on them for:
* site visit
* Depth, site, boat information
* pier set-up

h3. &nbsp;Methane seeps in July

&nbsp;--Going to the NE Santa Monica mound.&nbsp; 807m \~10-15m above seafloor.&nbsp; 100m across, 50m wide on top.&nbsp; Currents are 10cm/sec on top of mound.

5.25C

Must pick-up McStar sometime during cruise.

Also will have 4 gulper samplers--2 on swing arm, 2 on porch.

Much discussion on hydrate spontaneously forming and how it may impact DWSM.

&nbsp;Actions:
* Can we mimic hydrate formation in lab?&nbsp; unlikely.
* What are our contingencies if we form&nbsp; hydrate plug?&nbsp; Exhaust the intake tube from the back side?
* We could send a sample system down in March and see if you get hydrate formation.&nbsp;&nbsp;&nbsp;

h3.
Lab Stuff

&nbsp;Code:
* Gordon/Betty running the same firmware/software
* NEO \-\- super old stuff
* Bruce/Mack--running older stuff, but they are even different from each other (although that diff is small; could be just in the WCR protocol script)
* Moe--unknown what it has, as code has not been checked back into CVS in a long time

Plan:

Roll Bruce back to Oct, 2008 code and recreate a good DA run.

Push Mack forward so it's running Gordon/Betty code and see if that fixes sign inversion error.

Upgrade firmware on Moe to the latest.

Cheri will be helping with all this.


\-\- ]]></property>
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<property name="body"><![CDATA[# [Isotachophoresis]

2.&nbsp; List of filter manufacturers provided by Graham Marshall while at ALA (Jan, 2011)

http://www.idswater.com/water/us/spintek_filtration/ceramic_membrane/290_0/g_supplier_2.html
http://www.spintek.com/index.htm
http://www.refractron.com/filtration.asp
http://www.veoliawaterst.com/ceramem/en/
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TGK-4S73RD8-3&_user=10&_coverDate=07%2F15%2F2008&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1629826148&_rerunOrigin=google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=cc299542d01d8db163c75ce923f52a22&searchtype=a
http://www.ibmem.com/international/ceramic_membranes.htm
http://books.google.com/books?id=LpiuJVxJS_AC&pg=PA189&lpg=PA189&dq=ceramic+tubular+microfiltration&source=bl&ots=l2Dz6HXd66&sig=l094bOyDr3lIGWvvh4twe404HHY&hl=en&ei=MFpLTYv7Iou0sAOzl6HiCg&sa=X&oi=book_result&ct=result&resnum=7&sqi=2&ved=0CFMQ6AEwBg#v=onepage&q=ceramic%20tubular%20microfiltration&f=false
&nbsp;]]></property>
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<property name="body"><![CDATA[Copied from Email from Brent on 28 January 2010:


At LabAutomation 2010,
Juan Santiago of Stanford presented a talk called:
&nbsp;&nbsp; Rapid Chemical Detection and Identification with a Hand Held Device
Tuesday at 3:30 in the Evolving Apps of Lab Automation Track

The device was indeed small and powered by a USB port (<2.5 watts)

It detected pathogens in (aqueous) environmental samples via
isotachophoresis.

http://en.wikipedia.org/wiki/Isotachophoresis

Those molecules whose isotachophoresis separations would be similar could be
uniquely identified by their characteristic pKa values by repeating the
short (15 second or so) assay in buffers of differing pHs.

I thought the device might make a great "nose" for our ESP 3.

http://microfluidics.stanford.edu/
http://microfluidics.stanford.edu/Publications/Publications.html
http://microfluidics.stanford.edu/Publications/ElectrokineticFlows/schoch%20et%20al%20LoC%20extraction%20of%20RNA%20from%20lysate%202009.pdf

Is this worth pursuing further?]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]
# [May 20]
# [May 27]
# June 3
# June 10
# [June 17]
# June 24 \-\- Scott led
# July 1 \-\- Doug led
# [July 8]
# Jul 15 \--Preparation for Methane cruise
# Jul 22 \--Methane cruise
# Jul 29 \--Methane cruise
# [Aug 5]
# [Aug 12]
# [Aug 19]
# [Aug 26]
# [Sep 2]
# [Sep 9] \--CANON cruise, Scholin in England
# [Sep 16]
# Sep 12 \--prep for triple deployment
# [Sep 30]
# [Oct 7]
# Oct 14
# Oct 21
# Oct 28 \--Chris S @ WHOI, Jim at Pices
# [Nov 4]
# [Dec 2]
# [Dec 9]]]></property>
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<property name="body"><![CDATA[From Kloehn, these are custom syringes designed for us to operate down to 0C.

25 ml 29559 Rev A.  - near 0C these syringes will leak past the first seal but the second holds beyond -10C
10 ml 30367
2.5 ml 29558
1 ml 29557]]></property>
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<property name="body"><![CDATA[h3. &nbsp;Machine Builds

* Bruce has been run a lot and can't reproduce the processing error
* Seems to be an accumulation of something in the software (27May\--happening on Neo during deployment-\-more evidence it's software and not dwarf)
* HANDS
** Gordon's goes at 50% force (old ones worked at 30%)
** Betty taking 70% but with new frame works better than Gordon.

h3. MFB


h3. Drifter

* Test tank tomorrow (Friday).
* Dive days moved to 27 and 28 next week. Likely will only use the 27th.
* There will be no tension control on winch for June dive.
* Pressure transducer and moxa need mounting on lid
** need fitting and adaptor using power port on lid
** Mike P to make bracket for MOXA
** Roman to move mooring to high bay; Jim to get Ken Smith batteries
* Gene wants ESP 100lbs negative.&nbsp; Will work with Mike to accomplish.
* BRUCE is going in drifter

h3. Software

* &nbsp;

h3. Deep ESP


h6.

* Wand; don't have cables long enough for long wand assembly.&nbsp; Cables arrive 29th (too late)
* Will shoot for a 3' stubby.&nbsp; Code still to be developed
* TSV--needed tightening
* CPLD code works but needs testing
* Mink is soldered and waiting for modem before potting.
* D-ESP cleaning
** Doug has two 4" sections that can't be cleaned with toxicant.&nbsp; So idea is to add a filter puck taht we push tox through the core to clean both those lines in DWSM, then go to next SH1 run.

h3. GUI

* Will be loaded on Gordon and Betty for beta testing.

h3. Deployment Issues

For June:
* Mack in sphere
* Bruce in Drifter
* Moe on bench

h1. \\


h1. *September/October Mack and Bruce 2009*


h6. &nbsp; &nbsp; * See attachments for deployment calendar &nbsp;


h6. &nbsp;&nbsp;&nbsp; * If the code needs to be tweeked to use the V2 ctd or one surface ESP will not have a CTD


h6. &nbsp; &nbsp; * we need larger battery pack for ISUS to get high density sampling endurance


h6. &nbsp;&nbsp;&nbsp; * need to get dry and wet weight of drifter base before I put it back to standard


h6. &nbsp; &nbsp; * ESP and Iridium batteries


h3. &nbsp;Other Items:

* need loaner computer from IS for summer student&nbsp; (Cheri will put in request with IS for what we need)
Here is the schedule for the next two weeks:

* {gliffy:name=calendar\|space=ESPAPP\|page=21May2009\|pageid=10354699\|align=left\|size=L}
* 09may27=>&nbsp; There is water in one of the floats on the bail of the base used for the drifter.&nbsp; Need to check and drain before a shallow deployment of that base.]]></property>
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h4. {color:#ff00cc}SCRIPPS-Lab Run \-\- ESP-Waldo{color}

*&nbsp;April 27, 2015*

Roman delivers ESP Waldo to Andy Allen's lab at JCVI.&nbsp; Idea was to collect archived sample twice/week for \~6 months to test longevity issues with filters.

mid-June, instrument started losing comms to elevator dwarf.&nbsp; Roman sent down to replace dwarf on June 29-30. Re-canned and restarted mission.

RECOVERY

Roman recovers ESP-Waldo October 6, 2015.

h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce. Divers: Kim R., Paul C.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

Divers: Paul C., Jeff Sevadjian

{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload. Divers: Eric R, Jeff Sevadjian
\\

h4. {color:#ff00cc}1st MAKAI flight w 5 cartridges{color}

*July 22, 2015*

Flew triangle pattern after launch.&nbsp; Makai found chlorophyll feature, and we fired two cartridges while flying through.&nbsp; First cartridge may have had sticky valve and stayed in by-pass (filtered 1L in \~20 minutes; too fast).&nbsp; Second cartridge seemed to have worked.

Some issues with ESP not communicating it was on, and then LRAUV not turning it on.&nbsp; Went to recover vehicle late July 23, but did not surface until mission timed-out, after we were already ashore.&nbsp; That was when we discovered the comms issues.&nbsp; Fixed one, tried to fire during a 'night operation' Thursday evening.&nbsp; Discovered Friday morning a second comms issues, which was fixed, and fired the 3 samples during day on Friday, July 24.&nbsp; Did keep-station all weekend, and recovered LRAUV early Monday morning (July 27).

Results:

1.&nbsp; Cartridge #1 bypassed 1L (toroid valve stuck; sea water ran through instrument in bypass mode; 7 minutes); flying through feature (chl=3.0 ug/l; 10.97m)

2. &nbsp; #2 filtered 815.8ml; flying through feature (11.03m; chl=3.3 ug/l; took 53 minutes)

3. &nbsp; #3 filtered 802.3ml;&nbsp; within feature (13.8m; chl=3.02 ug/l; took 51 minutes)

4. &nbsp; #4 filtered 759.6ml,&nbsp; above feature (7.1m; chl=1.11 ug/l; took 50 minutes)

5.&nbsp;&nbsp; #5 filtered 809.1ml,&nbsp; below feature (19.4m; chl=4.24 ug/l; took 51 minutes)

Excellent summary paper by Yanwu Zhang about what the LRAUV did during this deployment-\-[here|^Zhang_etal_chlpeak.pdf|Yanwu's paper].(check your download folder)

h4. {color:#ff00cc}SCRIPPS-Del Mar Mooring \-\- ESP-Waldo{color}

*&nbsp;November 12, 2015*

Roman and Scott drive down Nov 8 and work for the week to assemble mooring.&nbsp; Goes in water on the 12th (check ESP-Waldo channel on Slack for pictures).&nbsp; Setup has SCRIPPS modem as master mooring controller.&nbsp; when it sends command string to ESP, ESP and ESP-modem awake, which allows us to get into ESP for diagnosis and large data transfers.&nbsp; At end of sampling, ESP and it's modem goes to sleep.&nbsp; Currently (Dec 1) using [this|^ESP deploy _DelMar_sampling_127.xlsx|Sampling schedule as of Dec 1] sampling schedule.

Dec 6, 2015

I2C error has stopped our sampling mission.&nbsp; ESP now providing only CTD updates.&nbsp; Brent's message:&nbsp; "The problem that surfaced first last Wednesday has recurred and is not going away this time.

Waldo's ESP host can access the sleepy microcontroller to get can status, etc., however, sleepy cannot access anything on the I2C bus."

Dec 14, 2015

I2C bus was back online\!&nbsp; Instrument had been left 'on' since last communications, and had some rough weather over this weekend.&nbsp; Brent was able to get in and unstick the hand then take a 'flawless' sample.&nbsp; Will see how she works in four days...

*Recovered Feb 4, 2016*.

h4. {color:#ff00cc}MAKAI flight w 4 Archives, 1 Lyse-n-go{color}

*Dec 18-21, 2015*

Launch/recover from MLML rib boat.&nbsp; Multiple failures with LRAUV; difficulty holding (shallow) depth, thruster errors. Original idea was to find a chl feature, take 2 archives.&nbsp; Dive below feature, take two archives.&nbsp; Reacquire feature, fire off l-n-g.&nbsp; With multiple vehicle errors and time running out (Holiday break; people leaving) we got one shallow archive, one deep, and ran the l-n-g deep.&nbsp; No feature ever found--very stormy and little stratification. Brett, Brian, Chris P on deployment; Brett, Ben, Jim on recovery.]]></property>
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<property name="body"><![CDATA[Present: Wayne, Cheri, Gene, Kevin, Jim, Doug, Scott
Absent: Addie, Chris S.

h3. Machine Builds

* History:  At end of last surface deployment with Bruce, near end of mission, PS and PC started losing position and going in wrong direction.
** Upon recovery, Cheri ran several hundred PS/PC moves and the error never repeated.
** Yesterday NEO (deployed) showed exact same error.  Cheri will watch; not enough time to have Brent dig into this issue.
** Cheri will check to see what bit version Bruce has (may not have the latest)
* Scott discovered dwarf/r-valve issue (1K resistor used instead of 100K);  Dwarfs in DWSM/D-ESP have already been changed.  This is a problem in +ALL+ ESP's, but unclear if it results in errors we see on Bruce and NEO.
* PC and CC springs on Bruce have been replaced.  Cheri noticed CC temp sensor needed replacement and is doing thermal calibration today.
* While temperature calibrating, will finish build of Gordon and Betty's hands.  Both should be installed by end of today.

h3. MFB

* PCR module #07 has arrived.

h3. Drifter

* Much discussion about whether Drifter will be ready for a core next week on Flyer cruise.  Many possible failure modes that we haven't had time to fully test.  Examples:
** lose control of cable and core goes too deep and gets crushed.
** what if we can't respool?  How to recover with 200m of line out.
** safety stop once core is pulled under buoy.  Breaking off the termination would not be a good thing.
** loss of communication; this state still needs to be coded

* Gene thinks that many of these problems will have fixes by next week, and thus having a core in the can for DAYTIME deployments would be an acceptable risk.  He is VERY uncomfortable leaving it through the night when we cannot watch it.  Much discussion ensued and we needed Science input (chris\!\!\!).  But the general consensus was one of high anxiety at the lack of testing of software control, and of core communications through same modem as Drifter control.  For that reason, we decided to go with an empty can/mooring, wired with pressure and accelerometer.  Scott will work with Mike P on preparing the can, lid, and mooring.

h3. Software

* Looks like changes to the dPress CPLD are working well.

h3. Deep ESP/DWSM

* Brent working on software.
* High Pressure test for DWSM leaks is tomorrow.  Doug working out how to tighten bells with minimum fuss.  Van will be cooled to 2C tonight, bells tightened tomorrow AM, and pressure raised to 3000psi at the intake port.  Minimum test is to see if anything leaks in upper bells.  may try and move valves.

h3. GUI

* Will be loaded on Gordon and Betty for beta testing.

h3. Deployment Issues

For June:
* Mack in sphere
* empty can on Drifter
* Moe on bench&nbsp; (and Bruce?)

h3. &nbsp;Other Items]]></property>
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<property name="body"><![CDATA[The original ESP GUI was a Java application that was connected to a SQL database.  Here are the use instructions for that application (some links don't work).
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.
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<property name="body"><![CDATA[For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
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h3.


h2. Topic:&nbsp; Is Axial cruise (Aug 16-26) tenable given what we've learned during recent Flyer cruise?
\\

h4. Present:&nbsp; Chris, Jim, Scott, Doug, Brent
\\

Discussion as to whether 7 weeks is enough time to address issues in the '[punch list|^4k Deep ESP Punch List.doc|stuff to do...]', and test D-ESP sufficiently for a successful deployment.&nbsp;

General idea is that it would be possible, but very difficult, and would jeopardize the Oct 1 MARS deployment.


&nbsp;Decision is that July 6 we will start having weekly check-in mtgs to make sure we are on track for a stress-free MARS deployment.]]></property>
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<property name="body"><![CDATA[Present: Wayne, Cheri, Kevin, Jim, Doug, Scott, Chris S

h3. Machine Builds

* CBV/AIV line length is incorrect and must be changed on Betty and Gordon.&nbsp; Was changed on Moe, but core function never checked afterward.&nbsp; This issue still needs to be checked on NEO.
* Currently:
** Gordon--has MFB attached but MFB running as a stand-alone.&nbsp; Easy to merge when ready but currently Monika using MFB and core can be run seperately.
** Betty--needs thermal calibration.&nbsp; Much discussion about appropriate cold test to do, and idea is to go to \-5C, after blowing all fluid out of Burkerts with dry N2.&nbsp; Idea is to test hand, carosel, clamps, elevator, but NOT run vlaves or syringes.
** Eventually Betty needs extended chemistry tests at 2C.&nbsp; To do this we need to build larger box (rectangle) to accomodate MFB on the core.&nbsp; This box must have access door.
** MOE--needs rectangle box, because Julie is ready for cold testing of PCR.&nbsp; Moe also needs temp calibration.

h3. MFB

* John Dzenitis (LLNL) is on vacation until 6-30.&nbsp; After that they will deliver 5 modules (7-6).&nbsp; Must confirm with them our total order of 12 modules with 8 spare heater elements.

h3. Drifter&nbsp;

* Drifter review this afternoon @ 1pm.



h3. Software

* Wayne taking a class at UC-B and has small class project.&nbsp; He is developing a Dwarf replacement; worried about power consumption, but looks like it may be only 20-30% higher than current dwarf, but with much more memory space.&nbsp; Wayne will talk to Scott and Brent about specifics, but class project is a go.
* Brent going to move the GUI branch onto the main branch, and then put the GUI code onto Gordon for exercise.
* Some concern as to why AIV calibration always seems to be 180degrees off.&nbsp; Brent wants to understand this and is on his to-do list.
* Syringe/sign inversion
** very difficult to duplicate in the lab so it's hard to study.&nbsp; One idea is that a bit gets set wrong that determines polarity.&nbsp; We currently don't have a way to query bit-state.&nbsp; We could take existing dwarf code and add debug ability, and it may let us see what's going on.&nbsp; Much discussion about what re-writing CPLD code and/or dwarf code might entail.&nbsp; Could be a time-sink; Scott/Brent/Wayne will get together on it.
** Discussion on whether we&nbsp; can have an error check/recovery that fixes this when it happens.&nbsp; Difficult, but Scott/Brent/Wayne to discuss.

h3. Deep ESP/DWSM

* Benthos modem issue.&nbsp; Boards ordered to replicate Hans Thomas' junction box will not work with the newer Benthos Universal Deck box.&nbsp; Jim working with Hans and Benthos to see if there is an electronic solution to problem.
* GG is going into ball to allow DWSM testing.
* Drop Wt--finished designing mechanism, and will wait on manufacture/mounting.
* Acoustic modem--not needed on MARS
* Toxicant bag--low on priority list for MARS deployment
* DWSM
** pressure transducers
*** a few will do simultaneous analog and serial output
*** must work to 2C, but most are not super cold-rated
*** Doug needs to know how we will read them.&nbsp; Talk to Scott
*** pricey ($2500/ea)
*** still getting lead times
** PISSER
*** schematic has been revised.&nbsp; Doug wants it reviewed before starts building.
** Overpressure valves
*** how will we read the contacts from the these valves?
*** will change current overpressure valves to larger ones we have on-hand.

h3. GUI

* Kevin working with Chris P to incorporate ESP parameters into GUI

h3. Deployment Issues


h3. &nbsp;Other Items]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]
# [Apr 12] \-\- Roman at WHOI, Chris P Europe
# Apr 19
# [Apr 26]
# [May 10]
# [May 17]
# May 24 \-\- Roman at WHOI, Chris S at WHOI, Chris P out
# [Jun 14] \-\- This has link to lysate dilution page
# [Jun 21]
# [Jun 28]
# Jul 5 \-\- MBARI closed
# [Jul 12] \-\- most of team at JdF]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://predator.shore.mbari.org/esp_gui/launch.jnlp]Project Documentation:

h3. Other Documents
# [Documents|ProjectDocuments]
# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
# [Presentations|ProjectPresentations]
# [Tasks]

]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://predator.shore.mbari.org/esp_gui/launch.jnlp]Project Documentation:

h3. Other Documents
# [Documents|ProjectDocuments]
# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
# [Presentations|ProjectPresentations]

]]></property>
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<property name="body"><![CDATA[# [4K Sphere]
# [Sable 5000 Iridium Beacon Manual v. 2.0|^Xeos_Sable_manual.pdf|v2.0]
# [Sable 5000 Iridium Beacon Manual v. 2.1|^Xeos_Sable_Manual_2.1.pdf|v2.1]]]></property>
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<property name="body"><![CDATA[# [4K Sphere]\\

h2. IEMI number for Sable 5000:


h1. 30002344


# [Sable 5000 Iridium Beacon Manual v. 2.0|^Xeos_Sable_manual.pdf|v2.0]
# [Sable 5000 Iridium Beacon Manual v. 2.1|^Xeos_Sable_Manual_2.1.pdf|v2.1]]]></property>
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<property name="body"><![CDATA[h3. Meeting Notes

# PDR Meeting (June 6, 2007)
## Attendees
### Rich Schramm
### Kevin Gomes
### Chris Scholin
### Doug Pargett
### Scott McLean
### Jim Birch
## Slides
## Demo Mockup
## WBS/Costs
]]></property>
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<property name="body"><![CDATA[User's Manuals
# [Quick Start Guide v1.2|^Xeos_Melo_manual-1.pdf|quick start]
# [User Manual v1.5|^Xeos_Melo_manual-2.pdf|Full Manual]
# [Watch Circle Console User Manual v2.1|^Xeos_Melo_manual-3.pdf|watch circle]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">18251924</id>
</property>
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<property name="body"><![CDATA[h2. IMEI number for the Melo tracker:


h3. *300034012090780*


User's Manuals
# [Quick Start Guide v1.2|^Xeos_Melo_manual-1.pdf|quick start]
# [User Manual v1.5|^Xeos_Melo_manual-2.pdf|Full Manual]
# [Watch Circle Console User Manual v2.1|^Xeos_Melo_manual-3.pdf|watch circle]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h4. {panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}

h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]
{panel}


{section}
{column:width=50%}

h4. {panel:title=Engineering|borderWidth=2}


h4. &nbsp;Generation 3

### [Requirements]
### [Detection Technologies]
### [Functional Requirements for Gen 3 ESP]
### [Development Leads]

h4. System Integration

### [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
### [Engineering Timeline] 2008
### [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
### [Cheat Sheet]
### [Container Storage Locker Information (10-1-2008)]
h4. Hardware

### [Deep ESP]
### Melo Iridium Tracker
### [Micro-Fluidics Block]
### [LLNL PCR heater module]
### [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
### [Sampling Wand Functional Req's] \- NEW -
### [DWSM--4k Deep Water Sampling Module]
### [Puck Numbering System]
### [Frit Identification system]
### [ISUS issues] (updated 31 Aug 2010)

h4. Software

### [Instrument Software Revision Level]
### [JIRA Bug Tracker|https://oceana.mbari.org/jira]
### [GUI Component Development Pages|2G ESP GUI Application]
### [ESP Image Analysis Application]
### [Power Commands (9-30-08)]
### [Radio Communication commands for tri-deployment (10-7-08)]
### [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
### [How To Get the ESP Software Running On Your Machine]
### [CVS For McLane]
### [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}

h4. {panel:title=Science|borderWidth=2}
### [2008 Deployments]
### [2009 Deployments]
### [2010 Deployments]
### [2011 Deployments]
#### [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
### [MFB-PCR distribution list] as of 4Nov2010
{panel}

{column}
{section}]]></property>
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h4. {panel:title=Administrative Items|borderWidth=2}
h3. {color:#009900}[ESP Logos]{color}
h2. Meeting notes
# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]
{panel}
{section}
{column:width=50%}
h4. {panel:title=Engineering|borderWidth=2}
h4. &nbsp;Generation 3
### [Requirements]
### [Detection Technologies]
### [Functional Requirements for Gen 3 ESP]
### [Development Leads]
h4. System Integration
### [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
### [Engineering Timeline] 2008
### [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
### [Cheat Sheet]
### [Container Storage Locker Information (10-1-2008)]
h4. Hardware
### [Deep ESP]
### [Melo Iridium Tracker]
### [Micro-Fluidics Block]
### [LLNL PCR heater module]
### [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
### [Sampling Wand Functional Req's] \- NEW -
### [DWSM--4k Deep Water Sampling Module]
### [Puck Numbering System]
### [Frit Identification system]
### [ISUS issues] (updated 31 Aug 2010)

h4. Software
### [Instrument Software Revision Level]
### [JIRA Bug Tracker|https://oceana.mbari.org/jira]
### [GUI Component Development Pages|2G ESP GUI Application]
### [ESP Image Analysis Application]
### [Power Commands (9-30-08)]
### [Radio Communication commands for tri-deployment (10-7-08)]
### [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
### [How To Get the ESP Software Running On Your Machine]
### [CVS For McLane]
### [Helpful DEBUGGING commands to discern machine state]
{panel}

{column}
{column:width=50%}

h4. {panel:title=Science|borderWidth=2}
### [2008 Deployments]
### [2009 Deployments]
### [2010 Deployments]
### [2011 Deployments]
#### [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
### [MFB-PCR distribution list] as of 4Nov2010
{panel}

{column}
{section}]]></property>
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h4. {panel:title=Administrative Items|BGcolor=blue|width=100%|borderWidth=4}

{panel}


h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]
{section}
{column:width=50%}

h4. {panel:title=Engineering|borderWidth=2}

{panel}


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# Melo Iridium Tracker
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{column}
{column:width=50%}

h4. {panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}

{column}
{section}]]></property>
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<property name="body"><![CDATA[h2. Notes

[~brian]: Here's a [UML of the current data model | ^ESP - Data Model UML.pdf]. A few things to note:

* I color coded classes by related groups. Cascading transactions work within related groups only, e.g. deleting an instrument will delete all the associated yellow classes only.
* I've written a basic CRUD test so I know that it can insert and delete trees of objects. Beyond that we'll have to work things out.
* At this point there is NO buisness logic implemented.  If a transaction breaks some database rule, for example, trying to insert a ConsumableAmount without a ConsumableType will throw an Exception.
* Collections are lazy loaded but I haven't written any unit tests to verify that they're working.
* I had some issues with the ConsumableAmount table. It's a many-to-many join table with an extra column for storing a value. JPA *hates* that. (You have to have the primary keys for both the ConsumableType and PhaseType *BEFORE* inserting the ConsumableAmount; so ConsumableAmount would've need to be handled is separate transactions.) The workaround was to add an id column; it's not pretty but it works. ]]></property>
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<property name="body"><![CDATA[h2. Notes

[~brian]: Here's a [UML of the current data model | ^ESP - Data Model UML.pdf]. A few things to note:

* I color coded classes by related groups. Cascading transactions work within related groups only, e.g. deleting an instrument will delete all the associated yellow classes only. I haven't tested out all the Cascade relations yet, so deleting an image might delete your instrument to :-). These should be easy fixes but I won't be able to write the tests until after my vacation sometime about 7/16.
* I've written a basic CRUD test so I know that it can insert and delete trees of objects. Beyond that we'll have to work things out.
* At this point there is NO buisness logic implemented.  If a transaction breaks some database rule, for example, trying to insert a ConsumableAmount without a ConsumableType, an Exception will be thrown.
* Collections are lazy loaded but I haven't written any unit tests to verify that they're working.
* I had some issues with the ConsumableAmount table. It's a many-to-many join table with an extra column for storing a value. JPA *hates* that. (You have to have the primary keys for both the ConsumableType and PhaseType *BEFORE* inserting the ConsumableAmount; so ConsumableAmount would've need to be handled is separate transactions.) The workaround was to add an id column; it's not pretty but it works. 
* All testing has been done against FOG. Is this copacetic or should I start setting up MySQL for developing against?]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{panel}
h4. {panel:title=Administrative Items|BGcolor=blue|width=100%|borderWidth=4}

h3. {color:#009900}[ESP Logos]{color}

h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]
{panel}
{section}
{column:width=50%}

{panel}
h4. {panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

### [Requirements]
### [Detection Technologies]
### [Functional Requirements for Gen 3 ESP]
### [Development Leads]

h4. System Integration

### [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
### [Engineering Timeline] 2008
### [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
### [Cheat Sheet]
### [Container Storage Locker Information (10-1-2008)]
h4. Hardware

### [Deep ESP]
### Melo Iridium Tracker
### [Micro-Fluidics Block]
### [LLNL PCR heater module]
### [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
### [Sampling Wand Functional Req's] \- NEW -
### [DWSM--4k Deep Water Sampling Module]
### [Puck Numbering System]
### [Frit Identification system]
### [ISUS issues] (updated 31 Aug 2010)

h4. Software

### [Instrument Software Revision Level]
### [JIRA Bug Tracker|https://oceana.mbari.org/jira]
### [GUI Component Development Pages|2G ESP GUI Application]
### [ESP Image Analysis Application]
### [Power Commands (9-30-08)]
### [Radio Communication commands for tri-deployment (10-7-08)]
### [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
### [How To Get the ESP Software Running On Your Machine]
### [CVS For McLane]
### [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}


h4. {panel:title=Science|borderWidth=2}
### [2008 Deployments]
### [2009 Deployments]
### [2010 Deployments]
### [2011 Deployments]
#### [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
### [MFB-PCR distribution list] as of 4Nov2010
{panel}

{column}
{section}]]></property>
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<property name="body"><![CDATA[h2. Notes

[~brian]: Here's a UML of the current data model. A few things to note:

* I color coded classes by related groups. Cascading transactions work within related groups only, e.g. deleting an instrument will delete all the associated yellow classes only.
* I've written a basic CRUD test so I know that it can insert and delete trees of objects. Beyond that we'll have to work things out.
* At this point there is NO buisness logic implemented.  If a transaction breaks some database rule, for example, trying to insert a ConsumableAmount without a ConsumableType will throw an Exception.
* Collections are lazy loaded but I haven't written any unit tests to verify that they're working.]]></property>
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<property name="body"><![CDATA[h2. Notes

[~brian]: Here's a [UML of the current data model | ^ESP - Data Model UML.pdf]. A few things to note:

* I color coded classes by related groups. Cascading transactions work within related groups only, e.g. deleting an instrument will delete all the associated yellow classes only.
* I've written a basic CRUD test so I know that it can insert and delete trees of objects. Beyond that we'll have to work things out.
* At this point there is NO buisness logic implemented.  If a transaction breaks some database rule, for example, trying to insert a ConsumableAmount without a ConsumableType will throw an Exception.
* Collections are lazy loaded but I haven't written any unit tests to verify that they're working.]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://predator.shore.mbari.org/esp_gui/launch.jnlp]Project Documentation:

h3. Other Documents
# [Documents|ProjectDocuments]
# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
# [Presentations|ProjectPresentations]
# [Tasks]

h3. Bug Tracking
# [JIRA Issue Tracker|http://oceana.shore.mbari.org:8082/browse/ESPAPP]

]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h4. {panel:title=Administrative Items|BGcolor=blue|width=100%|borderWidth=4}




h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]
{panel}

{section}
{column:width=50%}

h4. {panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}

h4. {panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}

{column}
{section}]]></property>
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<property name="body"><![CDATA[h3. Meeting Notes

# PDR Meeting (June 6, 2007)
## Attendees
### Rich Schramm
### Kevin Gomes
### Chris Scholin
### Doug Pargett
### Scott McLean
### Jim Birch
## Slides
## Demo Mockup
## WBS/Costs

h4. Memos
[Memo - 20070628 | Data Model Note]]]></property>
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<property name="body"><![CDATA[h3. Meeting Notes

# PDR Meeting (June 6, 2007)
## Attendees
### Rich Schramm
### Kevin Gomes
### Chris Scholin
### Doug Pargett
### Scott McLean
### Jim Birch
## Slides
## Demo Mockup
## WBS/Costs

h4. Memos
[Data Model Note | Memo - 20070628]]]></property>
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<property name="body"><![CDATA[Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note that we have yet to make a full batch of high-volume snap pucks, but when we do, those will be labeled 1HV (top and bottom).

Here is who is doing our etching:

LaserMark
2109 O'Toole Ave. Ste S
San Jose, CA 95131
Phone 408 433-9333
Fax 408 433-9343
\\
\\

Here is what I have packed up for etching:
| Type | Top/bottom | Numbered | Amount | NOTE |
| WCR | Top | 040-079 | 40 | \\ |
| \\ | Bottom | 040-079 | 40 | \\ |
| LAF | Top | 040-078 | 39 | 1=Missing |
| \\ | Bottom | 040-078 | 39 | 1=Missing |
| SAF | Top | 040-075 | 36 | 4sent to Gregg D |
| \\ | Bottom | 040-075 | 36 | 4sent to Gregg D |
| SHT | Top | 080-159 | 80 | \\ |
| SH1 | Bottom | 080-159 | 80 | \\ |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 390 | \\ |
\\
\\

I also sent 1 WCR puck (top&bottom) as a font sample.&nbsp; When these come back I will pack up the ones that are to be re-numbered(SHT2000-079).&nbsp; I haven't received a quote yet but Laser Mark said about $2 each piece + shipping.
\\

{color:#ff0000}UPDATE 3/24/08{color}

The SH1 tops that were misprinted are going to be sent out tomorrow to be re etched along with one of the LAF's that escaped detection last time:
| Type | Top/bottom | Numbered | Amount | NOTE |
| LAF | Top | 079 | 1 | Found the Lost 1\! |
| \\ | Bottom | 079 | 1 | \\ |
| SHT | Top | 000-079 | 80 | Old etching to be X'd out |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 82 | \\ |
That is all for now
\\
\\
\\

{color:#ff0000}UPDATE 2/24/09&nbsp; There have been several iterations of the above serialization process since this was last updated.{color}&nbsp;

Here is where we now stand:
| This   is an inventory of pucks that have been serialized and are available for   use.&nbsp; | \\ | \\ | \\ |
| There are   aprox. 1200 more pieces (or 600 more pucks) that have yet to be serialized. | \\ | \\ |
| They are   located in the 'B' building lab | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| Type | Top/Bottom | Lot 2 | Lot 2 | Lot 3 | Lot 3 | Lot 4 | Total | \\ |
| WCR | Top | 40 | 40 | 40 | 39 | 40 | 199 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 40 | 40 | 200 | \\ |
| LAF | Top | 40 | 40 | 40 | 38 | 40 | 198 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 36 | 40 | 196 | \\ |
| SAF | Top | 40 | 36 | 40 | 39 | 40 | 195 | \\ |
| \\ | Bottom | 40 | 36 | 40 | 40 | 40 | 196 | \\ |
| SHT | Top | 80 | 80 | 80 | 80 | 80 | 400 | \\ |
| SH1 \\ | Bottom | 80 | 80 | 80 | 77 | 80 | 397 | \\ |
| Total | \\ | 400 | 392 | 400 | 389 | 400 | 1981 | 990.5 |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | pieces | pucks |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| The   lot number refers to the 4th place in the serialization code:&nbsp; | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 letter type | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 1 digit lot number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 digit individual part number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| All parts   are numbered 000-079 ( except where some are missing) for each lot EXCEPT for : | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SHT=000-159 | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SH1=000-159 | \\ | \\ | \\ | \\ |
{color:#ff0000}{*}UPDATE August 11, 2010{*}{color}

&nbsp;Puck order from McLane arrived.

Rec'd&nbsp; 160 SH1, and 80 ea of LAF, SAF, WCR, HV (consists of HV top and SH1 bottom), all laser-etched.

PO 1010318
\\

Here is their email explaining their numbering system (sent Jan 14, 2010):
{Info:title=Useful Information}
{Info}
From: Tim Shanahan \[mailto:tshanahan@mclanelabs.com\]
Sent: Thursday, January 14, 2010 8:52 AM
To: 'Birch, James'
Cc: 'Pargett, Douglas'; 'Jensen, Scott'; Everlove, Cheri; 'Scholin, Chris';
Yuki Honjo (yhonjo@mclanelabs.com); Ivory Engstrom
(iengstrom@mclanelabs.com); Mike Mathewson (mathewson@mclanelabs.com)
Subject: Puck serial number format

Hello All,

We've been thinking about the serial number format for the pucks and we'd
like to suggest some modifications.&nbsp; I'm concerned about duplicating lot
numbers and the potential for having runs bigger than 1000 units.

At least for now, I think there's the possibility of McLane and MBARI still
continuing to make puck independently.&nbsp; Keeping track of the current lot
number could be problematic.

So I propose the following:

TTTMYYSSSS

TTT for type code as below.

MYY for date code in
M= 1 - 9 for Jan - Sept, A B or C for Oct Nov & Dec

YY for 2 digit year

SSSS for serial number 0000 - 9999

Also, this ensures that there never a letter I or O.

This increases the total number of characters from 7 to 10.
{info}
{info}
&nbsp;
\\
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<property name="body"><![CDATA[Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note that we have yet to make a full batch of high-volume snap pucks, but when we do, those will be labeled 1HV (top and bottom).

Here is who is doing our etching:

LaserMark
2109 O'Toole Ave. Ste S
San Jose, CA 95131
Phone 408 433-9333
Fax 408 433-9343
\\
\\

Here is what I have packed up for etching:
| Type | Top/bottom | Numbered | Amount | NOTE |
| WCR | Top | 040-079 | 40 | \\ |
| \\ | Bottom | 040-079 | 40 | \\ |
| LAF | Top | 040-078 | 39 | 1=Missing |
| \\ | Bottom | 040-078 | 39 | 1=Missing |
| SAF | Top | 040-075 | 36 | 4sent to Gregg D |
| \\ | Bottom | 040-075 | 36 | 4sent to Gregg D |
| SHT | Top | 080-159 | 80 | \\ |
| SH1 | Bottom | 080-159 | 80 | \\ |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 390 | \\ |
\\
\\

I also sent 1 WCR puck (top&bottom) as a font sample.&nbsp; When these come back I will pack up the ones that are to be re-numbered(SHT2000-079).&nbsp; I haven't received a quote yet but Laser Mark said about $2 each piece + shipping.
\\

{color:#ff0000}UPDATE 3/24/08{color}

The SH1 tops that were misprinted are going to be sent out tomorrow to be re etched along with one of the LAF's that escaped detection last time:
| Type | Top/bottom | Numbered | Amount | NOTE |
| LAF | Top | 079 | 1 | Found the Lost 1\! |
| \\ | Bottom | 079 | 1 | \\ |
| SHT | Top | 000-079 | 80 | Old etching to be X'd out |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 82 | \\ |
That is all for now
\\
\\
\\

{color:#ff0000}UPDATE 2/24/09&nbsp; There have been several iterations of the above serialization process since this was last updated.{color}&nbsp;

Here is where we now stand:
| This   is an inventory of pucks that have been serialized and are available for   use.&nbsp; | \\ | \\ | \\ |
| There are   aprox. 1200 more pieces (or 600 more pucks) that have yet to be serialized. | \\ | \\ |
| They are   located in the 'B' building lab | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| Type | Top/Bottom | Lot 2 | Lot 2 | Lot 3 | Lot 3 | Lot 4 | Total | \\ |
| WCR | Top | 40 | 40 | 40 | 39 | 40 | 199 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 40 | 40 | 200 | \\ |
| LAF | Top | 40 | 40 | 40 | 38 | 40 | 198 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 36 | 40 | 196 | \\ |
| SAF | Top | 40 | 36 | 40 | 39 | 40 | 195 | \\ |
| \\ | Bottom | 40 | 36 | 40 | 40 | 40 | 196 | \\ |
| SHT | Top | 80 | 80 | 80 | 80 | 80 | 400 | \\ |
| SH1 \\ | Bottom | 80 | 80 | 80 | 77 | 80 | 397 | \\ |
| Total | \\ | 400 | 392 | 400 | 389 | 400 | 1981 | 990.5 |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | pieces | pucks |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| The   lot number refers to the 4th place in the serialization code:&nbsp; | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 letter type | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 1 digit lot number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 digit individual part number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| All parts   are numbered 000-079 ( except where some are missing) for each lot EXCEPT for : | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SHT=000-159 | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SH1=000-159 | \\ | \\ | \\ | \\ |
{color:#ff0000}{*}UPDATE August 11, 2010{*}{color}

&nbsp;Puck order from McLane arrived.

Rec'd&nbsp; 160 SH1, and 80 ea of LAF, SAF, WCR, HV (consists of HV top and SH1 bottom), all laser-etched.


PO 1010318\\ \\]]></property>
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<property name="body"><![CDATA[Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note that we have yet to make a full batch of high-volume snap pucks, but when we do, those will be labeled 1HV (top and bottom).

Here is who is doing our etching:

LaserMark
2109 O'Toole Ave. Ste S
San Jose, CA 95131
Phone 408 433-9333
Fax 408 433-9343
\\
\\

Here is what I have packed up for etching:
| Type | Top/bottom | Numbered | Amount | NOTE |
| WCR | Top | 040-079 | 40 | \\ |
| \\ | Bottom | 040-079 | 40 | \\ |
| LAF | Top | 040-078 | 39 | 1=Missing |
| \\ | Bottom | 040-078 | 39 | 1=Missing |
| SAF | Top | 040-075 | 36 | 4sent to Gregg D |
| \\ | Bottom | 040-075 | 36 | 4sent to Gregg D |
| SHT | Top | 080-159 | 80 | \\ |
| SH1 | Bottom | 080-159 | 80 | \\ |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 390 | \\ |
\\
\\

I also sent 1 WCR puck (top&bottom) as a font sample.&nbsp; When these come back I will pack up the ones that are to be re-numbered(SHT2000-079).&nbsp; I haven't received a quote yet but Laser Mark said about $2 each piece + shipping.
\\

{color:#ff0000}UPDATE 3/24/08{color}

The SH1 tops that were misprinted are going to be sent out tomorrow to be re etched along with one of the LAF's that escaped detection last time:
| Type | Top/bottom | Numbered | Amount | NOTE |
| LAF | Top | 079 | 1 | Found the Lost 1\! |
| \\ | Bottom | 079 | 1 | \\ |
| SHT | Top | 000-079 | 80 | Old etching to be X'd out |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 82 | \\ |
That is all for now
\\
\\
\\

{color:#ff0000}UPDATE 2/24/09&nbsp; There have been several iterations of the above serialization process since this was last updated.{color}&nbsp;

Here is where we now stand:
| This   is an inventory of pucks that have been serialized and are available for   use.&nbsp; | \\ | \\ | \\ |
| There are   aprox. 1200 more pieces (or 600 more pucks) that have yet to be serialized. | \\ | \\ |
| They are   located in the 'B' building lab | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| Type | Top/Bottom | Lot 2 | Lot 2 | Lot 3 | Lot 3 | Lot 4 | Total | \\ |
| WCR | Top | 40 | 40 | 40 | 39 | 40 | 199 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 40 | 40 | 200 | \\ |
| LAF | Top | 40 | 40 | 40 | 38 | 40 | 198 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 36 | 40 | 196 | \\ |
| SAF | Top | 40 | 36 | 40 | 39 | 40 | 195 | \\ |
| \\ | Bottom | 40 | 36 | 40 | 40 | 40 | 196 | \\ |
| SHT | Top | 80 | 80 | 80 | 80 | 80 | 400 | \\ |
| SH1 \\ | Bottom | 80 | 80 | 80 | 77 | 80 | 397 | \\ |
| Total | \\ | 400 | 392 | 400 | 389 | 400 | 1981 | 990.5 |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | pieces | pucks |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| The   lot number refers to the 4th place in the serialization code:&nbsp; | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 letter type | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 1 digit lot number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 digit individual part number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| All parts   are numbered 000-079 ( except where some are missing) for each lot EXCEPT for : | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SHT=000-159 | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SH1=000-159 | \\ | \\ | \\ | \\ |
{color:#ff0000}{*}UPDATE August 11, 2010{*}{color}

&nbsp;Puck order from McLane arrived.

Rec'd&nbsp; 160 SH1, and 80 ea of LAF, SAF, WCR, HV (consists of HV top and SH1 bottom), all laser-etched.

PO 1010318
\\

Here is their email explaining their numbering system (sent Jan 14, 2010):
{Info:title=Mclane Numbering Scheme}

From: Tim Shanahan \[mailto:tshanahan@mclanelabs.com\]
Sent: Thursday, January 14, 2010 8:52 AM
To: 'Birch, James'
Cc: 'Pargett, Douglas'; 'Jensen, Scott'; Everlove, Cheri; 'Scholin, Chris';
Yuki Honjo (yhonjo@mclanelabs.com); Ivory Engstrom
(iengstrom@mclanelabs.com); Mike Mathewson (mathewson@mclanelabs.com)
Subject: Puck serial number format

Hello All,

We've been thinking about the serial number format for the pucks and we'd
like to suggest some modifications.&nbsp; I'm concerned about duplicating lot
numbers and the potential for having runs bigger than 1000 units.

At least for now, I think there's the possibility of McLane and MBARI still
continuing to make puck independently.&nbsp; Keeping track of the current lot
number could be problematic.

So I propose the following:

TTTMYYSSSS

TTT for type code as below.

MYY for date code in
M= 1 - 9 for Jan - Sept, A B or C for Oct Nov & Dec

YY for 2 digit year

SSSS for serial number 0000 - 9999

Also, this ensures that there never a letter I or O.

This increases the total number of characters from 7 to 10.
{info}

&nbsp;
\\
\\]]></property>
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<property name="body"><![CDATA[h1. Project Pages

Project Documentation:
# [Documents|ProjectDocuments]
# [Memos and Minutes|Project Memos Minutes]
# [Presentations|ProjectPresentations]

Related Project Sites:
# [GUI Web Start|http://predator.shore.mbari.org/esp_gui/launch.jnlp]]]></property>
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<property name="body"><![CDATA[h3. Meeting Notes

# PDR Meeting (June 6, 2007)
]]></property>
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<property name="body"><![CDATA[h3. Meeting Notes

# PDR Meeting (June 6, 2007)

## Attendees

### Rich Schramm
### Kevin Gomes

## Slides

## Demo Mockup

## WBS/Costs
]]></property>
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<property name="body"><![CDATA[h3. Meeting Notes

# PDR Meeting (June 6, 2007)
## Attendees
### Rich Schramm
### Kevin Gomes
## Slides
## Demo Mockup
## WBS/Costs
]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://predator.shore.mbari.org/esp_gui/launch.jnlp]Project Documentation:

h3. Other Documents
# [Documents|ProjectDocuments]
# [Memos and Minutes|Project Memos Minutes]
# [Presentations|ProjectPresentations]

]]></property>
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<property name="body"><![CDATA[# Attendees
## Chris Scholin
## Rich Schramm
## Brian Schlining
## Karen Salamy
## Kevin Gomes

# Notes
## Phases: HAB, BAC, LARV
## Phases run protocols
## Phase is a series of operations (could be one protocol, but more likely more).  Can be one puck, but more likely more.
## Phase is a standard set of operations
## Each protocol needs a puck (with filter)
## Filter may or may not have probes, whole cell has no probes, just brings home sample
## All pucks have serial numbers.
## pucks outer diameter is the same.
## there are different pucks for different
## SH = standard hybridization, detect molecules of interest. Heat it up and liquify.  Filter and then apply to SH2.  SH1 pucks can be used lysate.
## Why do we want to keep track of serial numbers on pucks
## Once puck is closed, not sure what is in there.
## Serial numbers help keep track of what they intend to use it for after build.
## Some have physical specimen and they need to figure out which puck has the specimen
## After filteration, put on another filter, then more chemistry, then image.
## Final PUCK is WCR (whole cell archival) is then sample is then preserved and brought home for shore side analysis
## Associated with probes is spot map (array map) ".Gal File" (what probe in what X,Y location).  Often listed as "Spot 23" then lookup with tell you X,Y
## Image is analyzed and you get intensities.
## Device can do "auto exposure" to figure out where it needs to be to get image in linear range of CCD chip.
## Also ask for constant exposure (do more than one constant exposure).
## Use standard curves and control spots on map.
## Standard curve is number of bugs/intensity
## Run exposure that you have standard curve for and then get intensity which then you lookup on the spot map.
## Low res images come across the wire (high res is 1MB).
## Phases can change the protocols (should we force users to use unique names- Chris thinks this would be good)
## Array map evolves.
## Protocols use same reagants, same amount 
## Phase-protocol combination (Phase tells you what the amounts are in the different protocols)
## Volumes filtered varies (tell it "Collect a liter", instrument decides how much until to filter until clogged)
## Print info comes from "gal file".  Old print is excel file.]]></property>
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<property name="body"><![CDATA[# Attendees
## Chris Scholin
## Rich Schramm
## Brian Schlining
## Karen Salamy
## Kevin Gomes

# Notes
## Phases: HAB, BAC, LARV
## Phases run protocols
## Phase is a series of operations (could be one protocol, but more likely more).  Can be one puck, but more likely more.
## Phase is a standard set of operations
## Each protocol needs a puck (with filter)
## Filter may or may not have probes, whole cell has no probes, just brings home sample
## All pucks have serial numbers.
## pucks outer diameter is the same.
## there are different pucks for different
## SH = standard hybridization, detect molecules of interest. Heat it up and liquify.  Filter and then apply to SH2.  SH1 pucks can be used lysate.
## Why do we want to keep track of serial numbers on pucks
## Once puck is closed, not sure what is in there.
## Serial numbers help keep track of what they intend to use it for after build.
## Some have physical specimen and they need to figure out which puck has the specimen
## After filteration, put on another filter, then more chemistry, then image.
## Final PUCK is WCR (whole cell archival) is then sample is then preserved and brought home for shore side analysis
## Associated with probes is spot map (array map) ".Gal File" (what probe in what X,Y location).  Often listed as "Spot 23" then lookup with tell you X,Y
## Image is analyzed and you get intensities.
## Device can do "auto exposure" to figure out where it needs to be to get image in linear range of CCD chip.
## Also ask for constant exposure (do more than one constant exposure).
## Use standard curves and control spots on map.
## Standard curve is number of bugs/intensity
## Run exposure that you have standard curve for and then get intensity which then you lookup on the spot map.
## Low res images come across the wire (high res is 1MB).
## Phases can change the protocols (should we force users to use unique names- Chris thinks this would be good)
## Array map evolves.
## Protocols use same reagants, same amount 
## Phase-protocol combination (Phase tells you what the amounts are in the different protocols)
## Volumes filtered varies (tell it "Collect a liter", instrument decides how much until to filter until clogged)
## Print info comes from "gal file".  Old print is excel file.
## Some filters are thrown away, some are archived.
## Comments also need to be captured.
## Events are "when we sample"
## User specifies start of phase
### Then delay (7 minutes let's say), then sample is taken (that is the actual "start").  The rest of the protocols depend on the environmental characteristics.
## There will be maximum time for each phase (can be shorter, never longer).
## Instrument capacities:
### Pucks: 
### Reagants: 20
### Waste: fixed in current machine
## Configuration file tells what reagents are at what valve.
## There is a waste 1 and waste 2 (NOTE this is dependent on the reagent. specify which waste reagent goes to)
## Power budget.
## Instrument run
### Take series of protocol, to build phases
### write high level script
### dervice max volumes.]]></property>
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<property name="body"><![CDATA[# Attendees
## Chris Scholin
## Rich Schramm
## Brian Schlining
## Karen Salamy
## Kevin Gomes

# Notes
## Phases: HAB, BAC, LARV
## Phases run protocols
## Phase is a series of operations (could be one protocol, but more likely more).  Can be one puck, but more likely more.
## Phase is a standard set of operations
## Each protocl needs a puck (with filter)
## Filter may or may not have probes, whole cell has no probes, just brings home sample
## All pucks have serial numbers.
## pucks outer diameter is the same.
## there are different pucks for different
## SH = standard hybridization, detect molecules of interest. Heat it up and liquify.  Filter and then apply to SH2.  SH1 pucks can be used lysate.
## Why do we want to keep track of serial numbers on pucks
## Once puck is closed, not sure what is in there.
## Serial numbers help keep track of what they intend to use it for after build.
## Some have physical specimen and they need to figure out which puck has the specimen
]]></property>
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<property name="body"><![CDATA[# Attendees
## Chris Scholin
## Rich Schramm
## Brian Schlining
## Karen Salamy
## Kevin Gomes

# Notes
## Phases: HAB, BAC, LARV
## Phases run protocols
## Phase is a series of operations (could be one protocol, but more likely more).  Can be one puck, but more likely more.
## Phase is a standard set of operations
## Each protocol needs a puck (with filter)
## Filter may or may not have probes, whole cell has no probes, just brings home sample
## All pucks have serial numbers.
## pucks outer diameter is the same.
## there are different pucks for different
## SH = standard hybridization, detect molecules of interest. Heat it up and liquify.  Filter and then apply to SH2.  SH1 pucks can be used lysate.
## Why do we want to keep track of serial numbers on pucks
## Once puck is closed, not sure what is in there.
## Serial numbers help keep track of what they intend to use it for after build.
## Some have physical specimen and they need to figure out which puck has the specimen
## After filteration, put on another filter, then more chemistry, then image.
## Final PUCK is WCR (whole cell archival) is then sample is then preserved and brought home for shore side analysis
## Associated with probes is spot map (array map) ".Gal File" (what probe in what X,Y location).  Often listed as "Spot 23" then lookup with tell you X,Y
## Image is analyzed and you get intensities.
## Device can do "auto exposure" to figure out where it needs to be to get image in linear range of CCD chip.
## Also ask for constant exposure (do more than one constant exposure).
## Use standard curves and control spots on map.
## Standard curve is number of bugs/intensity
## Run exposure that you have standard curve for and then get intensity which then you lookup on the spot map.
## Low res images come across the wire (high res is 1MB).
## Phases can change the protocols (should we force users to use unique names- Chris thinks this would be good)
## Array map evolves.
## Protocols use same reagants, same amount 
## Phase-protocol combination (Phase tells you what the amounts are in the different protocols)
## Volumes filtered varies (tell it "Collect a liter", instrument decides how much until to filter until clogged)
## Print info comes from "gal file".  Old print is excel file.
## Some filters are thrown away, some are archived.
## Comments also need to be captured.
## Events are "when we sample"
## User specifies start of phase
### Then delay (7 minutes let's say), then sample is taken (that is the actual "start").  The rest of the protocols depend on the environmental characteristics.
## There will be maximum time for each phase (can be shorter, never longer).
## Instrument capacities:
### Pucks: 
### Reagants: 20
### Waste: fixed in current machine
## Configuration file tells what reagents are at what valve.
## There is a waste 1 and waste 2 (NOTE this is dependent on the reagent. specify which waste reagent goes to)
## Power budget.
## Instrument run
### Take series of protocol, to build phases
### write high level script
### derive max volumes.
## Number of pucks is usual limitation
## sometimes waste can be limiter.]]></property>
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<property name="body"><![CDATA[This page lists some terminology and their definitions and context as they were used in the design work of the GUI application.  This is to ensure that when discussions are occurring, we are all talking about the same thing.
||Term||Definition||
|+*Mission*+|This is a logical span of time in which an ESP instrument is operating which has some start and end time.  It is usually associated with a the deployment and recovery of an ESP and consists of a sequence of phases.|
|+*Deployment*+|Is used synonymously with *Mission*|
|+*Mission Script*+|An ASCII file that contains Ruby commands that tell the ESP what actions to take at what times.|
|+*Phase*+|Consists of a cycle of instrument power up, a sequence of one or more protocol runs, and a power down.  Examples of phases are HAB, BAC, LARV, etc.  The concept of a phase is important as a mission script is defined using phases.  Phases can contain protocol run sequences that will take more than one sample of water. i.e. The relationship between phase and sample is one-to-many.|
|+*Sample Volume*+|A volume of water that is drawn into the instrument that contains the organisms which the instrument is attempting to identify. The volume of water is never actually stored in the instrument, it is run directly through a puck and filter and then sent to waste.|
|+*Lysate*+|A solution that is created by adding a solvent to the material that is filter out of the sample water by the filter.  This solution is then used as the source for protocol runs (and other).  In other words the lysate can be split amongst many protocol runs (and other events)|
|+*Protocol Run*+|Also just called _protocol_ or _assay_. Some named chemical protocol that yields data we wish to log. Each protocol run will have one puck, one filter and many images.|
|+*Puck*+|Metal ring that holds filter paper which is used to capture and process organisms|
|+*Filter*+|Special paper that is printed with various materials to help in detection of organisms. Not all filters have probes on them (for example, WCR has not probes as it just archives the organisms)|
|+*GAL File*+|File that is produced by the filter printer and contains the locations in X,Y coordinates and what probes are at those X,Y coordinates|
|+*Probe*+||
|+*SH*+|Acronym for Sandwich Hybridization|
|+*Standard Curve*+|A curve that maps intensity to density of organisms.  You use it to take the intensity of an image and calculate the density of organisms in the sample|
|+*Consumable*+|Is any resources on the instrument that can be consumed.  Examples are:
# Power
# Reagants
# Capacities like waste (there are 2)|

{gliffy:name=Phase|space=ESPAPP|page=Terminology|pageid=3114339|align=left|size=L}]]></property>
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<property name="body"><![CDATA[This page lists some terminology and their definitions and context as they were used in the design work of the GUI application.  This is to ensure that when discussions are occurring, we are all talking about the same thing.
||Term||Definition||
|+*Mission*+|This is a logical span of time in which an ESP instrument is operating which has some start and end time.  It is usually associated with a the deployment and recovery of an ESP and consists of a sequence of phases.|
|+*Deployment*+|Is used synonymously with *Mission*|
|+*Mission Script*+|An ASCII file that contains Ruby commands that tell the ESP what actions to take at what times.|
|+*Phase*+|Consists of a cycle of instrument power up, a sequence of one or more protocol runs, and a power down.  Examples of phases are HAB, BAC, LARV, etc.  The concept of a phase is important as a mission script is defined using phases.  Phases can contain protocol run sequences that will take more than one sample of water. i.e. The relationship between phase and sample is one-to-many.|
|+*Sample Volume*+|A volume of water that is drawn into the instrument that contains the organisms which the instrument is attempting to identify. The volume of water is never actually stored in the instrument, it is run directly through a puck and filter and then sent to waste.|
|+*Lysate*+|A solution that is created by adding a solvent to the material that is filter out of the sample water by the filter.  This solution is then used as the source for protocol runs (and other).  In other words the lysate can be split amongst many protocol runs (and other events)|
|+*Protocol Run*+|Also just called _protocol_ or _assay_. Some named chemical protocol that yields data we wish to log. Each protocol run will have one puck, one filter and many images.|
|+*Puck*+|Metal ring that holds filter paper which is used to capture and process organisms|
|+*Filter*+|Special paper that is printed with various materials to help in detection of organisms. Not all filters have probes on them (for example, WCR has not probes as it just archives the organisms)|
|+*GAL File*+|File that is produced by the filter printer and contains the locations in X,Y coordinates and what probes are at those X,Y coordinates|
|+*Probe*+||
|+*SH*+|Acronym for Sandwich Hybridization|
|+*Standard Curve*+|A curve that maps intensity to density of organisms.  You use it to take the intensity of an image and calculate the density of organisms in the sample|
|+*Consumable*+|Is any resources on the instrument that can be consumed.  Examples are:
# Power
# Reagants
# Capacities like waste (there are 2)|

{gliffy:name=Phase|space=ESPAPP|page=Terminology|pageid=3114339|align=left|size=L}]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Terminology|Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Terminology|ESPAPP:Terminology]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process.

h3. Requirements
|| Number || Requirement || Goal ||
| | User can define missions by specifying phases | Planning |
| | User can specify and adjust phase start times | Planning |
| | User can also specify a time to wait between events instead of a specific start time | Planning |
| | User can set mission start and end times that are not associated with a phase/protocol | Planning |
| | User can specify comments associated with missions that are printed at the top of the mission script | Planning |
| | After planning, application should generate mission script, puck loads, and reagent volumes | Planning |
| | User can add comments to a phase that will be generated in the script | Planning |
| | Users can add/delete/edit protocol runs and phases | Planning |
| | Users can add/delete/edit consumables | Planning |
| | Users can schedule Kills (end purges) or disable kills | Planning |
| | Users can define generic events and what script will actually be added to the master script (if needed) | Planning |
| | Mission plan generation will include a puck loading list | Planning |
| | User can associate external files with events (excel spreadsheet, documents, etc.) | Planning, Data Management |
| | Tide and phase information will be available | Planning, Data Management |
| | Application will list sample volumes with protocol run | Planning, Data Management |
| | User can add non-phase/protocol events (user defined) to the calendar anywhere | Data Management |
| | User can view images associated with phases | Data Management |
| | User can browse the .GAL file along with image and filter paper information | Data Management |
| | User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density | Data Management |
| | User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery | Data Management |
| | When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown | Data Management |
| | Application should allow for details of flushes to be seen/accounted for | Data Management |
| | The application should archive (and make available) the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts | Data Management |
| | Users should be able to download instrument logs and images and the GUI will parse out the following events:
* Track deployments of contextual sensors (sub-deployments of ESP)
* Collection of contextual sensor data (with capability to view/work with data) 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time | Data Management, State Visualization |
| | Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power | State Visualization |
| | Users can visualize the current state of the instrument | State Visualization |
| | Users can scroll back in time and visualize instrument state at the various points in time | State Visualization |

h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
{panel}
{column}
{section}
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument and the various places it will live.  The ESP directory structures contains the following:

# /var/log on the linux host is the root directory for the FTP site (i.e. = ftp://espName).
# /var/log/messages contains linux kernel messages
# /var/log/vsftpd.log records all FTP site traffic
# /var/log/$USER is top level output directory for each user's ESP data (can be overridden with $ESPlog variable, but this is rare)
# Content in /var/log depends on configuration, but default is:
## _hires_: high resolution camera images (each approx 3.5 MB)
## _lores_: low resolution camera images
## _midres_: medium resolution camera images (typically autoexposures)
## Top level directory contains default resolution camera images (typically fixed exposures)
# Only files in top level directory are uploaded to shore
# File types are:
## *.tif = TIFF camera images
## *.pcr = Comma Separated Value PCR Data
## *.out = Console output capture
### Text normally output to the esp interactive console
### Redirected here when running non-interactive mission script
### Can be viewed with showlog command
### File is named after operating mode (real, sim, simreal, quick)
## *.log = detailed, binary esp engineering logs.  The file is named after operating mode (real, sim, simreal, quick).  Can be viewed with dumplog.
## *.tube = list of carousel tubes processed
### One tube per line, last line is the currently active source tube
## ISUS*.err = ISUS error messages (direct from the ISUS)
## ISUS*.dat = text records of the ISUS data (complex and incorporates CTD data)
## CTD*.hex = CTD data in hexidecimal formatted text records
### Seabird specific format

NOTE: Brent wrote up some instructions on parsing the log file [here|ESPAPP:Parsing the Raw ESP Log File Format]

The initial thought about how a complete data management system might look is:
{section}
{column}
{gliffy:name=ESP Data Overview|space=ESPAPP|page=Design|pageid=6258757|align=left|size=M}
{column}
{column:width=60%}
{panel:title=Things to note}
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station (this includes the ruby scripts used to run the ESP).
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.
{panel}
{column}
{section}


So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

So, in order to manage this synchronization and storage of data, it was decided that the GUI would be reponsible for that synchronization.  Initially it would be a manual process as it will be time consuming and the user should be responsible for firing it off.  Then, once it is solidified a bit, it would be nice to push it back to a background thread that happens automatically.  The GUI for this synchronization, might look something like this:

{mockup:Data_Import|1}


Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

||Mockup||Notes||
|{mockup:Top Level|12}|A mockup of what the user might see upon first starting the application.|
|{mockup:InstrumentSelect|3}|Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?
Here is the mockup showing what might happen if the user selected one of the instruments.|
|{mockup:DeploymentSelect|3}|After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times|
|{mockup:MouseOverEvent|2}\\{mockup:EventDetails|2}|In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open.|




There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument and the various places it will live.  The ESP directory structures contains the following:

# /var/log on the linux host is the root directory for the FTP site (i.e. = ftp://espName).
# /var/log/messages contains linux kernel messages
# /var/log/vsftpd.log records all FTP site traffic
# /var/log/$USER is top level output directory for each user's ESP data (can be overridden with $ESPlog variable, but this is rare)
# Content in /var/log depends on configuration, but default is:
## _hires_: high resolution camera images (each approx 3.5 MB)
## _lores_: low resolution camera images
## _midres_: medium resolution camera images (typically autoexposures)
## Top level directory contains default resolution camera images (typically fixed exposures)
# Only files in top level directory are uploaded to shore
# File types are:
## *.tif = TIFF camera images
## *.pcr = Comma Separated Value PCR Data
## *.out = Console output capture
### Text normally output to the esp interactive console
### Redirected here when running non-interactive mission script
### Can be viewed with showlog command
### File is named after operating mode (real, sim, simreal, quick)
## *.log = detailed, binary esp engineering logs.  The file is named after operating mode (real, sim, simreal, quick).  Can be viewed with dumplog.
## *.tube = list of carousel tubes processed
### One tube per line, last line is the currently active source tube
## ISUS*.err = ISUS error messages (direct from the ISUS)
## ISUS*.dat = text records of the ISUS data (complex and incorporates CTD data)
## CTD*.hex = CTD data in hexidecimal formatted text records
### Seabird specific format

NOTE: Brent wrote up some instructions on parsing the log file [here|ESPAPP:Parsing the Raw ESP Log File Format]

The initial thought about how a complete data management system might look is:
{gliffy:name=ESP Data Overview|space=ESPAPP|page=Design|pageid=6258757|align=left|size=M}
{panel:title=Things to note}
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station (this includes the ruby scripts used to run the ESP).
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.
{panel}


So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

So, in order to manage this synchronization and storage of data, it was decided that the GUI would be reponsible for that synchronization.  Initially it would be a manual process as it will be time consuming and the user should be responsible for firing it off.  Then, once it is solidified a bit, it would be nice to push it back to a background thread that happens automatically.  The GUI for this synchronization, might look something like this:

{mockup:Data_Import|1}


Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

||Mockup||Notes||
|{mockup:Top Level|12}|A mockup of what the user might see upon first starting the application.|
|{mockup:InstrumentSelect|3}|Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?
Here is the mockup showing what might happen if the user selected one of the instruments.|
|{mockup:DeploymentSelect|3}|After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times|
|{mockup:MouseOverEvent|2}\\{mockup:EventDetails|2}|In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open.|




There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



]]></property>
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<property name="body"><![CDATA[Present:&nbsp;&nbsp; Brent, Jim, Scott, Chris S.

Absent: everyone else....
\\

h2. &nbsp;Issues:

McLane joined us via phone for first part of meeting.
* Learned that host board we sent was only 8MB, and would not work for them.&nbsp; Although we typically use 16MB boards, the smaller boards should have worked.&nbsp; They are ordering 16MB board and will have it shipped to us.&nbsp; Brent to check it out.
* Camera issues.&nbsp; New cameras have pixel shift in bottom 2-3 rows of pixels.&nbsp; powering on/off usually removes this.&nbsp; Much more testing needs to be done to approve the newer cameras.&nbsp; MBARI (Brent) will do this testing, to begin as soon as we receive the host board from them.&nbsp; Scott has ideas on how to supply 12V power to the newer cameras.&nbsp; Once we get the board, anticipate 1 week of testing.
* We'd like to piggy-back on the temperature sensor board order McLane is about to make.&nbsp; Order 10 boards; 5 stuffed, 5 PCB's.&nbsp; Also 20 backing mounts for these boards.
* We will notify Ivory of the blue-wire fix for the ESD problem Scott discovered on Betty.

h5. +Machines+


h6. Bruce

Has new firmware, but there are issues with calibration.&nbsp; Tina using currently--will try and squeeze in b/w her runs and recalibrate (Scott).

h6. Mack

currently on Drifter.&nbsp; Just learned it has loose PSV, and was blowing out WCR, so nothing collected.&nbsp; Still needs firmware update.

h6. MOE

&nbsp;has latest firmware (v3.7).

still has pressure issues--several issues:* pressure gauge changes over time; possible PEEK creep causing it.&nbsp; we will turn down gain to increase the head space of the gauges
* snap pucks come apart
** clamp isn't strong enough.&nbsp; Scott to talk to Doug about spring change.&nbsp; Also will run clamp w/heat to see if PEEK changes more.
** &nbsp;
h6. NEO

currently in water at M0. will get latest firmware when recovered (Aug 30)

Must decide what Science wants to do with NEO.&nbsp; Will there be a pier deployment in Oct/Nov, and do we rid NEO of the tombstone and replace with an MFB and the attendant firmware upgrades, so all cores will be running the same thing?&nbsp; Discuss this at next Tuesday's science mtg.


h6. Gordon

Still in the ball.&nbsp; Chris P. hopes to be finished with post-cruise QC runs by Monday.

h6. Betty

still not ready for science checkout.&nbsp; Pressure issues among others.


h3. Communications for BIOSPACE

&nbsp;Question is whether one antenna on Brent's house can hit both the bight and the shadow ESP position.&nbsp; Plan is for him to get a wider angle antenna (not omni) and shoot it down the middle, or almost so, and try and hit both positions.&nbsp; Has a sailing friend who heads out every Weds who can take some radio gear and go to each GPS coordinate and see if Brent can ping the boat from his home.


h2.]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]
# [May 20]
# [May 27]
# June 3
# June 10
# [June 17]
# June 24 \-\- Scott led
# July 1 \-\- Doug led
# [July 8]
# Jul 15 --Preparation for Methane cruise
# Jul 22 --Methane cruise
# Jul 29 --Methane cruise 
# [Aug 5]]]></property>
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process.

h3. Requirements
|| Number || Requirement || Goal ||
| | User can define missions by specifying phases | Planning |
| | User can specify and adjust phase start times | Planning |
| | User can also specify a time to wait between events instead of a specific start time | Planning |
| | User can set mission start and end times that are not associated with a phase/protocol | Planning |
| | User can specify comments associated with missions that are printed at the top of the mission script | Planning |
| | After planning, application should generate mission script, puck loads, and reagent volumes | Planning |
| | User can add comments to a phase that will be generated in the script | Planning |
| | Users can add/delete/edit protocol runs and phases | Planning |
| | Users can add/delete/edit consumables | Planning |
| | Users can schedule Kills (end purges) or disable kills | Planning |
| | Users can define generic events and what script will actually be added to the master script (if needed) | Planning |
| | User can associate external files with events (excel spreadsheet, documents, etc.) | Planning, Data Management |
| | Tide and phase information will be available | Planning, Data Management |
| | Application will list sample volumes with protocol run | Planning, Data Management |
| | User can add non-phase/protocol events (user defined) to the calendar anywhere | Data Management |
| | User can view images associated with phases | Data Management |
| | User can browse the .GAL file along with image and filter paper information | Data Management |
| | User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density | Data Management |
| | User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery | Data Management |
| | When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown | Data Management |
| | Application should allow for details of flushes to be seen/accounted for | Data Management |
| | The application should archive (and make available) the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts | Data Management |
| | Users should be able to download instrument logs and images and the GUI will parse out the following events:
* Track deployments of contextual sensors (sub-deployments of ESP)
* Collection of contextual sensor data (with capability to view/work with data) 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time | Data Management, State Visualization |
| | Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power | State Visualization |
| | Users can visualize the current state of the instrument | State Visualization |
| | Users can scroll back in time and visualize instrument state at the various points in time | State Visualization |

h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
{panel}
{column}
{section}
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<property name="body"><![CDATA[h2. Notes

[~brian]: Here's a [UML of the current data model | ^ESP - Data Model UML.pdf]. A few things to note:

* I color coded classes by related groups. Cascading transactions work within related groups only, e.g. deleting an instrument will delete all the associated yellow classes only. I haven't tested out all the Cascade relations yet, so deleting an image might delete your instrument to :-). These should be easy fixes but I won't be able to write the tests until after my vacation sometime about 7/16.
* I've written a basic CRUD test so I know that it can insert and delete trees of objects. Beyond that we'll have to work things out.
* At this point there is NO buisness logic implemented.  If a transaction breaks some database rule, for example, trying to insert a ConsumableAmount without a ConsumableType, an Exception will be thrown.
* Collections are lazy loaded but I haven't written any unit tests to verify that they're working.
* I had some issues with the ConsumableAmount table. It's a many-to-many join table with an extra column for storing a value. JPA *hates* that. (You have to have the primary keys for both the ConsumableType and PhaseType *BEFORE* inserting the ConsumableAmount; so ConsumableAmount would've need to be handled is separate transactions.) The workaround was to add an id column; it's not pretty but it works. 
* All testing has been done against FOG. Is this copacetic or should I start setting up MySQL for developing against?
* All transactions are currently handled through a single EAO object.
* The ESP-DAL (<- Data Access Layer) build uses Maven 2. A dependency graph is available at [here | ^ESP - Data Model Dependencies.png]]]></property>
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<property name="body"><![CDATA[h2. Notes

[~brian]: Here's a [UML of the current data model | ^ESP - Data Model UML.pdf]. A few things to note:

* I color coded classes by related groups. Cascading transactions work within related groups only, e.g. deleting an instrument will delete all the associated yellow classes only. I haven't tested out all the Cascade relations yet, so deleting an image might delete your instrument to :-). These should be easy fixes but I won't be able to write the tests until after my vacation sometime about 7/16.
* I've written a basic CRUD test so I know that it can insert and delete trees of objects. Beyond that we'll have to work things out.
* At this point there is NO buisness logic implemented.  If a transaction breaks some database rule, for example, trying to insert a ConsumableAmount without a ConsumableType, an Exception will be thrown.
* Collections are lazy loaded but I haven't written any unit tests to verify that they're working.
* I had some issues with the ConsumableAmount table. It's a many-to-many join table with an extra column for storing a value. JPA *hates* that. (You have to have the primary keys for both the ConsumableType and PhaseType *BEFORE* inserting the ConsumableAmount; so ConsumableAmount would've need to be handled is separate transactions.) The workaround was to add an id column; it's not pretty but it works. 
* All testing has been done against FOG. Is this copacetic or should I start setting up MySQL for developing against?
* All transactions are currently handled through a single EAO object.
* The ESP-DAL (<- Data Access Layer) build uses Maven 2. A dependency graph is available at [here | ^ESP - Data Model Dependencies.png]

[~kgomes]: Some questions I have about the model
* What sort of things go in Event_Types?  I think we are using those for mostly stuff that gets parsed out of the log file and stuffed into events, but should we have Protocol_Run, Phases, or Deployments in the event types even though they are actually subclasses?
* I think the Eventt hierarchy should look like Deployment->Phases->Protocol_Runs.  Just want to verify.]]></property>
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<property name="body"><![CDATA[This page lists some terminology and their definitions and context as they were used in the design work of the GUI application.  This is to ensure that when discussions are occurring, we are all talking about the same thing.
||Term||Definition||
| +*Sample Volume*+ | A volume of water that is drawn into the instrument that contains the organisms which the instrument is attempting to identify. The volume of water is never actually stored in the instrument, it is run directly through a puck and filter and then sent to waste. |
| +*Probe Array*+ | |
| +*Filter*+ | Special paper that is used to filter out suspended material from a water sample. Sometimes the filter has probe arrays printed on it, but not always (for example, WCR has no probes as it just archives the organisms). |
| +*GAL File*+ | File that is produced by the filter printer and contains the locations in X,Y coordinates and what probe arrays are at those X,Y coordinates. |
| +*Puck*+ | Metal ring that holds filter paper which is used to capture and process organisms. There are three types of pucks:
# Standard Volume Sample puck (SVS)
# High Volume Sample puck (HVS)
# Whole Cell Archive (WCR) |
| +*Collection Stage*+ | The location where a puck is loaded during sample collection. |
| +*Carousel*+ | Rotating set of tubes where pucks are stored. |
| +*Manipulator*+ | The mechanism which is used to move pucks to the various locations in the ESP. |
| +*Lysate*+ | A solution that is created by adding a solvent to the material that is filtered out of the sample water by the filter.  This solution is then used as the source for analysis.  Note the lysate can be split amongst many protocol runs (and other events). |
| +*Protocol*+ | This is a sequence of steps that are taken to perform some biological analysis. This is sometimes called an Assay. |
| +*Protocol Run*+ | This is the actual execution of a defined protocol. |
| +*Phase*+ | Consists of a cycle of instrument power up, a sequence of one or more protocol runs, and a power down.  Examples of phases are HAB, BAC, LARV, etc.  The concept of a phase is important as a mission script is defined using phases.  Phases can contain protocol run sequences that will take more than one sample of water. i.e. The relationship between phase and sample is one-to-many. Note also that the ESP normally goes into a low power, or quiescent, state. |
| +*Inital Purge*+ | When a phase begins, the ESP powers up and initializes itself.  If disinfectant solution was used in the previous phase, it will need to be purged by running a step called +*Initial Purge*+. |
| +*Mission*+ | This is a logical span of time in which an ESP instrument is operating which has some start and end time.  It is usually associated with a deployment and recovery of an ESP and consists of a sequence of phases separated by quiescent states. |
| +*Deployment*+ | Is used synonymously with *Mission* |
| +*Mission Script*+ | An ASCII file that contains Ruby commands that tell the ESP what actions to take at what times. |
| +*SH*+ | Acronym for Sandwich Hybridization |
| +*Standard Curve*+ | A curve that maps intensity to density of organisms.  You use it to take the intensity of an image and calculate the density of organisms in the sample. |
| +*Consumable*+ | Is any resource on the instrument that can be consumed.  Examples are:
# Power
# Reagants
# Capacities like waste (there are 2)|

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<property name="body"><![CDATA[This page lists some terminology and their definitions and context as they were used in the design work of the GUI application.  This is to ensure that when discussions are occurring, we are all talking about the same thing.
||Term||Definition||
| +*Sample Volume*+ | A volume of water that is drawn into the instrument that contains the organisms which the instrument is attempting to identify. The volume of water is never actually stored in the instrument, it is run directly through a puck and filter and then sent back out to the environment. |
| +*Probe Array*+ | |
| +*Filter*+ | Special paper that is used to filter out suspended material from a water sample. Sometimes the filter has probe arrays printed on it, but not always (for example, WCR has no probes as it just archives the organisms). |
| +*GAL File*+ | File that is produced by the filter printer and contains the locations in X,Y coordinates and what probe arrays are at those X,Y coordinates. |
| +*Puck*+ | Metal ring that holds filter paper which is used to capture and process organisms. There are three types of pucks:
# Standard Volume Sample puck (SVS)
# High Volume Sample puck (HVS)
# Whole Cell Archive (WCR) |
| +*Collection Stage*+ | The location where a puck is loaded during sample collection. |
| +*Carousel*+ | Rotating set of tubes where pucks are stored. |
| +*Manipulator*+ | The mechanism which is used to move pucks to the various locations in the ESP. |
| +*Lysate*+ | A solution that is created by adding a solvent to the material that is filtered out of the sample water by the filter.  This solution is then used as the source for analysis.  Note the lysate can be split amongst many protocol runs (and other events). |
| +*Protocol*+ | This is a sequence of steps that are taken to perform some biological analysis. This is sometimes called an Assay. |
| +*Protocol Run*+ | This is the actual execution of a defined protocol. |
| +*Phase*+ | Consists of a cycle of instrument power up, a sequence of one or more protocol runs, and a power down.  Examples of phases are HAB, BAC, LARV, etc.  The concept of a phase is important as a mission script is defined using phases.  Phases can contain protocol run sequences that will take more than one sample of water. i.e. The relationship between phase and sample is one-to-many. Note also that the ESP normally goes into a low power, or quiescent, state. |
| +*Inital Purge*+ | When a phase begins, the ESP powers up and initializes itself.  If disinfectant solution was used in the previous phase, it will need to be purged by running a step called +*Initial Purge*+. |
| +*Mission*+ | This is a logical span of time in which an ESP instrument is operating which has some start and end time.  It is usually associated with a deployment and recovery of an ESP and consists of a sequence of phases separated by quiescent states. |
| +*Deployment*+ | Is used synonymously with *Mission* |
| +*Mission Script*+ | An ASCII file that contains Ruby commands that tell the ESP what actions to take at what times. |
| +*SH*+ | Acronym for Sandwich Hybridization |
| +*Standard Curve*+ | A curve that maps intensity to density of organisms.  You use it to take the intensity of an image and calculate the density of organisms in the sample. |
| +*Consumable*+ | Is any resource on the instrument that can be consumed.  Examples are:
# Power
# Reagants
# Capacities like waste (there are 2)|

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<property name="body"><![CDATA[This page lists some terminology and their definitions and context as they were used in the design work of the GUI application.  This is to ensure that when discussions are occurring, we are all talking about the same thing.
||Term||Definition||
| +*Sample Volume*+ | A volume of water that is drawn into the instrument that contains the organisms which the instrument is attempting to identify. The volume of water is never actually stored in the instrument, it is run directly through a puck and filter and then sent to waste. |
| +*Probe Array*+ | |
| +*Filter*+ | Special paper that is used to filter out suspended material from a water sample. Sometimes the filter has probe arrays printed on it, but not always (for example, WCR has no probes as it just archives the organisms). |
| +*GAL File*+ | File that is produced by the filter printer and contains the locations in X,Y coordinates and what probe arrays are at those X,Y coordinates. |
| +*Puck*+ | Metal ring that holds filter paper which is used to capture and process organisms. |
| +*Lysate*+ | A solution that is created by adding a solvent to the material that is filtered out of the sample water by the filter.  This solution is then used as the source for analysis.  Note the lysate can be split amongst many protocol runs (and other events). |
| +*Protocol*+ | This is a sequence of steps that are taken to perform some biological analysis. This is sometimes called an Assay. |
| +*Protocol Run*+ | This is the actual execution of a defined protocol. |
| +*Phase*+ | Consists of a cycle of instrument power up, a sequence of one or more protocol runs, and a power down.  Examples of phases are HAB, BAC, LARV, etc.  The concept of a phase is important as a mission script is defined using phases.  Phases can contain protocol run sequences that will take more than one sample of water. i.e. The relationship between phase and sample is one-to-many. Note also that the ESP normally goes into a low power, or quiescent, state. |
| +*Mission*+ | This is a logical span of time in which an ESP instrument is operating which has some start and end time.  It is usually associated with a deployment and recovery of an ESP and consists of a sequence of phases separated by quiescent states. |
| +*Deployment*+ | Is used synonymously with *Mission* |
| +*Mission Script*+ | An ASCII file that contains Ruby commands that tell the ESP what actions to take at what times. |
| +*SH*+ | Acronym for Sandwich Hybridization |
| +*Standard Curve*+ | A curve that maps intensity to density of organisms.  You use it to take the intensity of an image and calculate the density of organisms in the sample. |
| +*Consumable*+ | Is any resource on the instrument that can be consumed.  Examples are:
# Power
# Reagants
# Capacities like waste (there are 2)|

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<property name="body"><![CDATA[This page lists some terminology and their definitions and context as they were used in the design work of the GUI application.  This is to ensure that when discussions are occurring, we are all talking about the same thing.
||Term||Definition||
| +*Sample Volume*+ | A volume of water that is drawn into the instrument that contains the organisms which the instrument is attempting to identify. The volume of water is never actually stored in the instrument, it is run directly through a puck and filter and then sent to waste. |
| +*Probe Array*+ | |
| +*Filter*+ | Special paper that is used to filter out suspended material from a water sample. Sometimes the filter has probe arrays printed on it, but not always (for example, WCR has no probes as it just archives the organisms). |
| +*GAL File*+ | File that is produced by the filter printer and contains the locations in X,Y coordinates and what probe arrays are at those X,Y coordinates. |
| +*Puck*+ | Metal ring that holds filter paper which is used to capture and process organisms. |
| +*Collection Stage*+ | The location where a puck is loaded during sample collection. |
| +*Carousel*+ | Rotating set of tubes where pucks are stored. |
| +*Manipulator*+ | The mechanism which is used to move pucks to the various locations in the ESP. |
| +*Lysate*+ | A solution that is created by adding a solvent to the material that is filtered out of the sample water by the filter.  This solution is then used as the source for analysis.  Note the lysate can be split amongst many protocol runs (and other events). |
| +*Protocol*+ | This is a sequence of steps that are taken to perform some biological analysis. This is sometimes called an Assay. |
| +*Protocol Run*+ | This is the actual execution of a defined protocol. |
| +*Phase*+ | Consists of a cycle of instrument power up, a sequence of one or more protocol runs, and a power down.  Examples of phases are HAB, BAC, LARV, etc.  The concept of a phase is important as a mission script is defined using phases.  Phases can contain protocol run sequences that will take more than one sample of water. i.e. The relationship between phase and sample is one-to-many. Note also that the ESP normally goes into a low power, or quiescent, state. |
| +*Inital Purge*+ | When a phase begins, the ESP powers up and initializes itself.  If disinfectant solution was used in the previous phase, it will need to be purged by running a step called +*Initial Purge*+. |
| +*Mission*+ | This is a logical span of time in which an ESP instrument is operating which has some start and end time.  It is usually associated with a deployment and recovery of an ESP and consists of a sequence of phases separated by quiescent states. |
| +*Deployment*+ | Is used synonymously with *Mission* |
| +*Mission Script*+ | An ASCII file that contains Ruby commands that tell the ESP what actions to take at what times. |
| +*SH*+ | Acronym for Sandwich Hybridization |
| +*Standard Curve*+ | A curve that maps intensity to density of organisms.  You use it to take the intensity of an image and calculate the density of organisms in the sample. |
| +*Consumable*+ | Is any resource on the instrument that can be consumed.  Examples are:
# Power
# Reagants
# Capacities like waste (there are 2)|

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<property name="body"><![CDATA[This page lists some terminology and their definitions and context as they were used in the design work of the GUI application.  This is to ensure that when discussions are occurring, we are all talking about the same thing.
||Term||Definition||
| +*Probe Array*+ | |
| +*Filter*+ | Special paper that is used to filter out suspended material from a water sample. Sometime the filter has probe arrays printed on it, but not always (for example, WCR has not probes as it just archives the organisms). |
| +*GAL File*+ |File that is produced by the filter printer and contains the locations in X,Y coordinates and what probe arrays are at those X,Y coordinates|
| +*Puck*+ | Metal ring that holds filter paper which is used to capture and process organisms. |
| +*Protocol*+ | This is a sequence of steps that are taken to perform some biological analysis. This is sometimes called an Assay. |
| +*Protocol Run*+ | This is the actual execution of a defined protocol |
| +*Mission*+ | This is a logical span of time in which an ESP instrument is operating which has some start and end time.  It is usually associated with a the deployment and recovery of an ESP and consists of a sequence of phases. |
| +*Deployment*+ | Is used synonymously with *Mission* |
| +*Mission Script*+ | An ASCII file that contains Ruby commands that tell the ESP what actions to take at what times. |
|+*Phase*+|Consists of a cycle of instrument power up, a sequence of one or more protocol runs, and a power down.  Examples of phases are HAB, BAC, LARV, etc.  The concept of a phase is important as a mission script is defined using phases.  Phases can contain protocol run sequences that will take more than one sample of water. i.e. The relationship between phase and sample is one-to-many.|
|+*Sample Volume*+|A volume of water that is drawn into the instrument that contains the organisms which the instrument is attempting to identify. The volume of water is never actually stored in the instrument, it is run directly through a puck and filter and then sent to waste.|
|+*Lysate*+|A solution that is created by adding a solvent to the material that is filter out of the sample water by the filter.  This solution is then used as the source for protocol runs (and other).  In other words the lysate can be split amongst many protocol runs (and other events)|
|+*SH*+|Acronym for Sandwich Hybridization|
|+*Standard Curve*+|A curve that maps intensity to density of organisms.  You use it to take the intensity of an image and calculate the density of organisms in the sample|
|+*Consumable*+|Is any resources on the instrument that can be consumed.  Examples are:
# Power
# Reagants
# Capacities like waste (there are 2)|

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<property name="body"><![CDATA[This page lists some terminology and their definitions and context as they were used in the design work of the GUI application.  This is to ensure that when discussions are occurring, we are all talking about the same thing.
||Term||Definition||
| +*Sample Volume*+ | A volume of water that is drawn into the instrument that contains the organisms which the instrument is attempting to identify. The volume of water is never actually stored in the instrument, it is run directly through a puck and filter and then sent to waste. |
| +*Probe Array*+ | |
| +*Filter*+ | Special paper that is used to filter out suspended material from a water sample. Sometime the filter has probe arrays printed on it, but not always (for example, WCR has not probes as it just archives the organisms). |
| +*GAL File*+ |File that is produced by the filter printer and contains the locations in X,Y coordinates and what probe arrays are at those X,Y coordinates|
| +*Puck*+ | Metal ring that holds filter paper which is used to capture and process organisms. |
| +*Lysate*+ | A solution that is created by adding a solvent to the material that is filtered out of the sample water by the filter.  This solution is then used as the source for analysis.  Note the lysate can be split amongst many protocol runs (and other events) |
| +*Protocol*+ | This is a sequence of steps that are taken to perform some biological analysis. This is sometimes called an Assay. |
| +*Protocol Run*+ | This is the actual execution of a defined protocol |
| +*Mission*+ | This is a logical span of time in which an ESP instrument is operating which has some start and end time.  It is usually associated with a the deployment and recovery of an ESP and consists of a sequence of phases. |
| +*Deployment*+ | Is used synonymously with *Mission* |
| +*Mission Script*+ | An ASCII file that contains Ruby commands that tell the ESP what actions to take at what times. |
|+*Phase*+|Consists of a cycle of instrument power up, a sequence of one or more protocol runs, and a power down.  Examples of phases are HAB, BAC, LARV, etc.  The concept of a phase is important as a mission script is defined using phases.  Phases can contain protocol run sequences that will take more than one sample of water. i.e. The relationship between phase and sample is one-to-many.|
|+*SH*+|Acronym for Sandwich Hybridization|
|+*Standard Curve*+|A curve that maps intensity to density of organisms.  You use it to take the intensity of an image and calculate the density of organisms in the sample|
|+*Consumable*+|Is any resources on the instrument that can be consumed.  Examples are:
# Power
# Reagants
# Capacities like waste (there are 2)|

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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process:

h3. Requirements
||Number||Requirement||Associated View||
|1|User can define missions by specifying phases|Planning|
|2|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|Be able to add non-phase/protocol events (user defined) to the calendar anywhere|Operation|
|5|Be able to set mission start end times that are not associated with a phase/protocol|Planning|
|6|Be able to specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User shall be able to add comments to a phase that will be generated in the script|Planning|
|8|User shall be able to view images associated with phases|Operation|
|9|User shall be able to browse the .GAL file along with image and filter paper information|Operation|
|10|User should be able to browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Operation|
|11|User should be able to browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Operation|
|12|User should be able to associate external files with events (excel spreadsheet, documents, etc.)|Planning,Operation|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|Operation|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users should have a form to add/delete/edit protocol runs and phases|Planning|
|16|Users should have a form to add/delete/edit consumables|Planning|
|17|In application users should have sample volume listed with protocol run|Planning|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should somehow be shown|Operation|
|19|Tide and phase information should be available during planning|Planning,Operation|
|20|Application should allow for details of flushes to be seen/accounted for|Operation|
|21|Users should be able to schedule Kills (end purges) or disable kills|Planning|
|22|Users should be able to define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to download instrument logs and images and the GUI will parse out the following events: 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time|Operation|
|24|Users should be able to visualize the current state of the instrument|Operation,State|
|25|Users should be able to scroll back in time and visualize instrument state at the various points in time|State|
|26|The application should archive the environment variables for each deployment.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts|Operation|


h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual Meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
{panel}
{column}
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process:

h3. Requirements
||Number||Requirement||Associated View||
|1|User can define missions by specifying phases|Planning|
|2|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|Be able to add non-phase/protocol events (user defined) to the calendar anywhere|Operation|
|5|Be able to set mission start end times that are not associated with a phase/protocol|Planning|
|6|Be able to specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User shall be able to add comments to a phase that will be generated in the script|Planning|
|8|User shall be able to view images associated with phases|Operation|
|9|User shall be able to browse the .GAL file along with image and filter paper information|Operation|
|10|User should be able to browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Operation|
|11|User should be able to browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Operation|
|12|User should be able to associate external files with events (excel spreadsheet, documents, etc.)|Planning,Operation|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|Operation|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users should have a form to add/delete/edit protocol runs and phases|Planning|
|16|Users should have a form to add/delete/edit consumables|Planning|
|17|In application users should have sample volume listed with protocol run|Planning|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should somehow be shown|Operation|
|19|Tide and phase information should be available during planning|Planning,Operation|
|20|Application should allow for details of flushes to be seen/accounted for|Operation|
|21|Users should be able to schedule Kills (end purges) or disable kills|Planning|
|22|Users should be able to define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to download instrument logs and images and the GUI will parse out the following events: 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time|Operation|
|24|Users should be able to visualize the current state of the instrument|Operation,State|
|25|Users should be able to scroll back in time and visualize instrument state at the various points in time|State|
|26|The application should archive the environment variables for each deployment.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts|Operation|


h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from User Manual Meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual Meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process:

h3. Requirements
||Number||Requirement||Goal||
|1|User can define missions by specifying phases|Planning|
|2|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|User can add non-phase/protocol events (user defined) to the calendar anywhere|Data Management|
|5|User can set mission start and end times that are not associated with a phase/protocol|Planning|
|6|User can specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User can add comments to a phase that will be generated in the script|Planning|
|8|User can view images associated with phases|Data Management|
|9|User can browse the .GAL file along with image and filter paper information|Data Management|
|10|User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Data Management|
|11|User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Data Management|
|12|User can associate external files with events (excel spreadsheet, documents, etc.)|Planning,Data Mangement|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|State Visualization|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users can add/delete/edit protocol runs and phases|Planning|
|16|Users can add/delete/edit consumables|Planning|
|17|Application will list sample volumes with protocol run|Planning, Data Management|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown|Data Management|
|19|Tide and phase information will be available|Planning,Data Management|
|20|Application should allow for details of flushes to be seen/accounted for|Data Management|
|21|Users can schedule Kills (end purges) or disable kills|Planning|
|22|Users can define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to download instrument logs and images and the GUI will parse out the following events: 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time|Operation|
|24|Users can visualize the current state of the instrument|State Visualization|
|25|Users can scroll back in time and visualize instrument state at the various points in time|State Visualization|
|26|The application should archive the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts|Data Management|


h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# 
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process:

h3. Requirements
||Number||Requirement||Goal||
|1|User can define missions by specifying phases|Planning|
|2|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|User can add non-phase/protocol events (user defined) to the calendar anywhere|Data Management|
|5|User can set mission start and end times that are not associated with a phase/protocol|Planning|
|6|User can specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User can add comments to a phase that will be generated in the script|Planning|
|8|User can view images associated with phases|Data Management|
|9|User can browse the .GAL file along with image and filter paper information|Data Management|
|10|User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Data Management|
|11|User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Data Management|
|12|User can associate external files with events (excel spreadsheet, documents, etc.)|Planning,Data Mangement|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|State Visualization|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users can add/delete/edit protocol runs and phases|Planning|
|16|Users can add/delete/edit consumables|Planning|
|17|Application will list sample volumes with protocol run|Planning, Data Management|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown|Data Management|
|19|Tide and phase information will be available|Planning,Data Management|
|20|Application should allow for details of flushes to be seen/accounted for|Data Management|
|21|Users can schedule Kills (end purges) or disable kills|Planning|
|22|Users can define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to download instrument logs and images and the GUI will parse out the following events: 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time|Operation|
|24|Users can visualize the current state of the instrument|State Visualization|
|25|Users can scroll back in time and visualize instrument state at the various points in time|State Visualization|
|26|The application should archive the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts|Data Management|


h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
{panel}
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process:

h3. Requirements
||Number||Requirement||Goal||
|1|User can define missions by specifying phases|Planning|
|2|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|User can add non-phase/protocol events (user defined) to the calendar anywhere|Data Management|
|5|User can set mission start and end times that are not associated with a phase/protocol|Planning|
|6|User can specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User can add comments to a phase that will be generated in the script|Planning|
|8|User can view images associated with phases|Data Management|
|9|User can browse the .GAL file along with image and filter paper information|Data Management|
|10|User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Data Management|
|11|User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Data Management|
|12|User can associate external files with events (excel spreadsheet, documents, etc.)|Planning,Data Mangement|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|State Visualization|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users can add/delete/edit protocol runs and phases|Planning|
|16|Users can add/delete/edit consumables|Planning|
|17|Application will list sample volumes with protocol run|Planning, Data Management|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown|Data Management|
|19|Tide and phase information will be available|Planning,Data Management|
|20|Application should allow for details of flushes to be seen/accounted for|Data Management|
|21|Users can schedule Kills (end purges) or disable kills|Planning|
|22|Users can define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to download instrument logs and images and the GUI will parse out the following events: 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time|Operation|
|24|Users can visualize the current state of the instrument|State Visualization|
|25|Users can scroll back in time and visualize instrument state at the various points in time|State Visualization|
|26|The application should archive the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts|Data Management|


h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual Meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=60%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=40%}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


]]></property>
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<property name="body"><![CDATA[h2. Notes

[~brian]: Here's a [UML of the current data model | ^ESP - Data Model UML.pdf]. A few things to note:

* I color coded classes by related groups. Cascading transactions work within related groups only, e.g. deleting an instrument will delete all the associated yellow classes only. I haven't tested out all the Cascade relations yet, so deleting an image might delete your instrument to :-). These should be easy fixes but I won't be able to write the tests until after my vacation sometime about 7/16.
* I've written a basic CRUD test so I know that it can insert and delete trees of objects. Beyond that we'll have to work things out.
* At this point there is NO buisness logic implemented.  If a transaction breaks some database rule, for example, trying to insert a ConsumableAmount without a ConsumableType, an Exception will be thrown.
* Collections are lazy loaded but I haven't written any unit tests to verify that they're working.
* I had some issues with the ConsumableAmount table. It's a many-to-many join table with an extra column for storing a value. JPA *hates* that. (You have to have the primary keys for both the ConsumableType and PhaseType *BEFORE* inserting the ConsumableAmount; so ConsumableAmount would've need to be handled is separate transactions.) The workaround was to add an id column; it's not pretty but it works. 
* All testing has been done against FOG. Is this copacetic or should I start setting up MySQL for developing against?
* All transactions are currently handled through a single EAO object.]]></property>
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<property name="body"><![CDATA[h2. Notes

[~brian]: Here's a [UML of the current data model | ^ESP - Data Model UML.pdf]. A few things to note:

* I color coded classes by related groups. Cascading transactions work within related groups only, e.g. deleting an instrument will delete all the associated yellow classes only. I haven't tested out all the Cascade relations yet, so deleting an image might delete your instrument to :-). These should be easy fixes but I won't be able to write the tests until after my vacation sometime about 7/16.
* I've written a basic CRUD test so I know that it can insert and delete trees of objects. Beyond that we'll have to work things out.
* At this point there is NO buisness logic implemented.  If a transaction breaks some database rule, for example, trying to insert a ConsumableAmount without a ConsumableType, an Exception will be thrown.
* Collections are lazy loaded but I haven't written any unit tests to verify that they're working.
* I had some issues with the ConsumableAmount table. It's a many-to-many join table with an extra column for storing a value. JPA *hates* that. (You have to have the primary keys for both the ConsumableType and PhaseType *BEFORE* inserting the ConsumableAmount; so ConsumableAmount would've need to be handled is separate transactions.) The workaround was to add an id column; it's not pretty but it works. 
* All testing has been done against FOG. Is this copacetic or should I start setting up MySQL for developing against?
* All transactions are currently handled through a single EAO object.
* The ESP-DAL (<- Data Access Layer) build uses Maven 2.]]></property>
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<property name="body"><![CDATA[h4. (as of Jan 7, 2013)



h3. Surface Mooring Cables

25.5m (bare)

25.3m (bare)

21.5m (w/ floats)

15.6m (w/ floats)


15.2m (w/ floats)


h3. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them. ]]></property>
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<property name="body"><![CDATA[h2. Notes

[~brian]: Here's a [UML of the current data model | ^ESP - Data Model UML.pdf]. A few things to note:

* I color coded classes by related groups. Cascading transactions work within related groups only, e.g. deleting an instrument will delete all the associated yellow classes only. I haven't tested out all the Cascade relations yet, so deleting an image might delete your instrument to :-). These should be easy fixes but I won't be able to write the tests until after my vacation sometime about 7/16.
* I've written a basic CRUD test so I know that it can insert and delete trees of objects. Beyond that we'll have to work things out.
* At this point there is NO buisness logic implemented.  If a transaction breaks some database rule, for example, trying to insert a ConsumableAmount without a ConsumableType, an Exception will be thrown.
* Collections are lazy loaded but I haven't written any unit tests to verify that they're working.
* I had some issues with the ConsumableAmount table. It's a many-to-many join table with an extra column for storing a value. JPA *hates* that. (You have to have the primary keys for both the ConsumableType and PhaseType *BEFORE* inserting the ConsumableAmount; so ConsumableAmount would've need to be handled is separate transactions.) The workaround was to add an id column; it's not pretty but it works. 
* All testing has been done against FOG. Is this copacetic or should I start setting up MySQL for developing against?
* All transactions are currently handled through a single EAO object.
* The ESP-DAL (<- Data Access Layer) build uses Maven 2. A dependency graph is available at [here | ESP - Data Model Dependencies.png]]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=60%}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}


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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


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# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation. Done in three stages
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}


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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 18 Feb 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [MFB-PCR distribution list] as of 14Jun2010]]></property>
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<property name="body"><![CDATA[Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note that we have yet to make a full batch of high-volume snap pucks, but when we do, those will be labeled 1HV (top and bottom).

Here is who is doing our etching:

LaserMark
2109 O'Toole Ave. Ste S
San Jose, CA 95131
Phone 408 433-9333
Fax 408 433-9343
\\
\\

Here is what I have packed up for etching:
| Type | Top/bottom | Numbered | Amount | NOTE |
| WCR | Top | 040-079 | 40 | \\ |
| \\ | Bottom | 040-079 | 40 | \\ |
| LAF | Top | 040-078 | 39 | 1=Missing |
| \\ | Bottom | 040-078 | 39 | 1=Missing |
| SAF | Top | 040-075 | 36 | 4sent to Gregg D |
| \\ | Bottom | 040-075 | 36 | 4sent to Gregg D |
| SHT | Top | 080-159 | 80 | \\ |
| SH1 | Bottom | 080-159 | 80 | \\ |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 390 | \\ |
\\
\\

I also sent 1 WCR puck (top&bottom) as a font sample.&nbsp; When these come back I will pack up the ones that are to be re-numbered(SHT2000-079).&nbsp; I haven't received a quote yet but Laser Mark said about $2 each piece + shipping.
\\

{color:#ff0000}UPDATE 3/24/08{color}

The SH1 tops that were misprinted are going to be sent out tomorrow to be re etched along with one of the LAF's that escaped detection last time:
| Type | Top/bottom | Numbered | Amount | NOTE |
| LAF | Top | 079 | 1 | Found the Lost 1\! |
| \\ | Bottom | 079 | 1 | \\ |
| SHT | Top | 000-079 | 80 | Old etching to be X'd out |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 82 | \\ |
That is all for now
\\
\\
\\

{color:#ff0000}UPDATE 2/24/09&nbsp; There have been several iterations of the above serialization process since this was last updated.{color}&nbsp;

Here is where we now stand:
| This   is an inventory of pucks that have been serialized and are available for   use.&nbsp; | \\ | \\ | \\ |
| There are   aprox. 1200 more pieces (or 600 more pucks) that have yet to be serialized. | \\ | \\ |
| They are   located in the 'B' building lab | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| Type | Top/Bottom | Lot 2 | Lot 2 | Lot 3 | Lot 3 | Lot 4 | Total | \\ |
| WCR | Top | 40 | 40 | 40 | 39 | 40 | 199 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 40 | 40 | 200 | \\ |
| LAF | Top | 40 | 40 | 40 | 38 | 40 | 198 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 36 | 40 | 196 | \\ |
| SAF | Top | 40 | 36 | 40 | 39 | 40 | 195 | \\ |
| \\ | Bottom | 40 | 36 | 40 | 40 | 40 | 196 | \\ |
| SHT | Top | 80 | 80 | 80 | 80 | 80 | 400 | \\ |
| SH1 \\ | Bottom | 80 | 80 | 80 | 77 | 80 | 397 | \\ |
| Total | \\ | 400 | 392 | 400 | 389 | 400 | 1981 | 990.5 |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | pieces | pucks |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| The   lot number refers to the 4th place in the serialization code:&nbsp; | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 letter type | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 1 digit lot number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 digit individual part number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| All parts   are numbered 000-079 ( except where some are missing) for each lot EXCEPT for : | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SHT=000-159 | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SH1=000-159 | \\ | \\ | \\ | \\ |]]></property>
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process.

h3. Requirements
|| Number || Requirement || Goal ||
| | User can define missions by specifying phases | Planning |
| | User can specify and adjust phase start times | Planning |
| | User can also specify a time to wait between events instead of a specific start time | Planning |
| | User can set mission start and end times that are not associated with a phase/protocol | Planning |
| | User can specify comments associated with missions that are printed at the top of the mission script | Planning |
| | After planning, application should generate mission script, puck loads, and reagent volumes | Planning |
| | User can add comments to a phase that will be generated in the script | Planning |
| | Users can add/delete/edit protocol runs and phases | Planning |
| | Users can add/delete/edit consumables | Planning |
| | Users can schedule Kills (end purges) or disable kills | Planning |
| | Users can define generic events and what script will actually be added to the master script (if needed) | Planning |
| | User can associate external files with events (excel spreadsheet, documents, etc.) | Planning, Data Management |
| | Tide and phase information will be available | Planning, Data Management |
| | Application will list sample volumes with protocol run | Planning, Data Management |
| | User can add non-phase/protocol events (user defined) to the calendar anywhere | Data Management |
| | User can view images associated with phases | Data Management |
| | User can browse the .GAL file along with image and filter paper information | Data Management |
| | User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density | Data Management |
| | User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery | Data Management |
| | When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown | Data Management |
| | Application should allow for details of flushes to be seen/accounted for | Data Management |
| | The application should archive (and make available) the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts | Data Management |
| | Users should be able to download instrument logs and images and the GUI will parse out the following events:
* Track deployments of contextual sensors (sub-deployments of ESP)
* Collection of contextual sensor data (with capability to view/work with data) 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time | Data Management, State Visualization |
| | Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power | State Visualization |
| | Users can visualize the current state of the instrument | State Visualization |
| | Users can scroll back in time and visualize instrument state at the various points in time | State Visualization |

h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
{panel}
{column}
{section}
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process:

h3. Requirements
|| Number || Requirement || Goal ||
| | User can define missions by specifying phases | Planning |
| | User can specify and adjust phase start times | Planning |
| | User can also specify a time to wait between events instead of a specific start time | Planning |
| | User can set mission start and end times that are not associated with a phase/protocol | Planning |
| | User can specify comments associated with missions that are printed at the top of the mission script | Planning |
| | After planning, application should generate mission script, puck loads, and reagent volumes | Planning |
| | User can add comments to a phase that will be generated in the script | Planning |
| | Users can add/delete/edit protocol runs and phases | Planning |
| | Users can add/delete/edit consumables | Planning |
| | Users can schedule Kills (end purges) or disable kills | Planning |
| | Users can define generic events and what script will actually be added to the master script (if needed) | Planning |
| | User can associate external files with events (excel spreadsheet, documents, etc.) | Planning, Data Management |
| | Tide and phase information will be available | Planning, Data Management |
| | Application will list sample volumes with protocol run | Planning, Data Management |
| | User can add non-phase/protocol events (user defined) to the calendar anywhere | Data Management |
| | User can view images associated with phases | Data Management |
| | User can browse the .GAL file along with image and filter paper information | Data Management |
| | User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density | Data Management |
| | User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery | Data Management |
| | When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown | Data Management |
| | Application should allow for details of flushes to be seen/accounted for | Data Management |
| | The application should archive (and make available) the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts | Data Management |
| | Users should be able to download instrument logs and images and the GUI will parse out the following events:
* Track deployments of contextual sensors (sub-deployments of ESP)
* Collection of contextual sensor data (with capability to view/work with data) 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time | Data Management, State Visualization |
| | Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power | State Visualization |
| | Users can visualize the current state of the instrument | State Visualization |
| | Users can scroll back in time and visualize instrument state at the various points in time | State Visualization |

h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
{panel}
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process.

h3. Requirements
|| Number || Requirement || Goal ||
| | User can define missions by specifying phases | Planning |
| | User can specify and adjust phase start times | Planning |
| | User can also specify a time to wait between events instead of a specific start time | Planning |
| | User can set mission start and end times that are not associated with a phase/protocol | Planning |
| | User can specify comments associated with missions that are printed at the top of the mission script | Planning |
| | After planning, application should generate mission script, puck loads, and reagent volumes | Planning |
| | User can add comments to a phase that will be generated in the script | Planning |
| | Users can add/delete/edit protocol runs and phases | Planning |
| | Users can add/delete/edit consumables | Planning |
| | Users can schedule Kills (end purges) or disable kills | Planning |
| | Users can define generic events and what script will actually be added to the master script (if needed) | Planning |
| | User can associate external files with events (excel spreadsheet, documents, etc.) | Planning, Data Management |
| | Tide and phase information will be available | Planning, Data Management |
| | Application will list sample volumes with protocol run | Planning, Data Management |
| | User can add non-phase/protocol events (user defined) to the calendar anywhere | Data Management |
| | User can view images associated with phases | Data Management |
| | User can browse the .GAL file along with image and filter paper information | Data Management |
| | User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density | Data Management |
| | User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery | Data Management |
| | When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown | Data Management |
| | Application should allow for details of flushes to be seen/accounted for | Data Management |
| | The application should archive (and make available) the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts | Data Management |
| | Users should be able to download instrument logs and images and the GUI will parse out the following events:
* Track deployments of contextual sensors (sub-deployments of ESP)
* Collection of contextual sensor data (with capability to view/work with data) 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time | Data Management, State Visualization |
| | Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power | State Visualization |
| | Users can visualize the current state of the instrument | State Visualization |
| | Users can scroll back in time and visualize instrument state at the various points in time | State Visualization |

h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
{panel}
{column}
{section}
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process:

h3. Requirements
||Number||Requirement||Goal||
|#|User can define missions by specifying phases|Planning|
|#|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|User can add non-phase/protocol events (user defined) to the calendar anywhere|Data Management|
|5|User can set mission start and end times that are not associated with a phase/protocol|Planning|
|6|User can specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User can add comments to a phase that will be generated in the script|Planning|
|8|User can view images associated with phases|Data Management|
|9|User can browse the .GAL file along with image and filter paper information|Data Management|
|10|User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Data Management|
|11|User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Data Management|
|12|User can associate external files with events (excel spreadsheet, documents, etc.)|Planning,Data Mangement|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|State Visualization|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users can add/delete/edit protocol runs and phases|Planning|
|16|Users can add/delete/edit consumables|Planning|
|17|Application will list sample volumes with protocol run|Planning, Data Management|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown|Data Management|
|19|Tide and phase information will be available|Planning,Data Management|
|20|Application should allow for details of flushes to be seen/accounted for|Data Management|
|21|Users can schedule Kills (end purges) or disable kills|Planning|
|22|Users can define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to download instrument logs and images and the GUI will parse out the following events: 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time|Operation|
|24|Users can visualize the current state of the instrument|State Visualization|
|25|Users can scroll back in time and visualize instrument state at the various points in time|State Visualization|
|26|The application should archive the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts|Data Management|


h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process:

h3. Requirements
||Number||Requirement||Goal||
| # |User can define missions by specifying phases|Planning|
| # |User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|User can add non-phase/protocol events (user defined) to the calendar anywhere|Data Management|
|5|User can set mission start and end times that are not associated with a phase/protocol|Planning|
|6|User can specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User can add comments to a phase that will be generated in the script|Planning|
|8|User can view images associated with phases|Data Management|
|9|User can browse the .GAL file along with image and filter paper information|Data Management|
|10|User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Data Management|
|11|User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Data Management|
|12|User can associate external files with events (excel spreadsheet, documents, etc.)|Planning,Data Mangement|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|State Visualization|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users can add/delete/edit protocol runs and phases|Planning|
|16|Users can add/delete/edit consumables|Planning|
|17|Application will list sample volumes with protocol run|Planning, Data Management|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown|Data Management|
|19|Tide and phase information will be available|Planning,Data Management|
|20|Application should allow for details of flushes to be seen/accounted for|Data Management|
|21|Users can schedule Kills (end purges) or disable kills|Planning|
|22|Users can define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to download instrument logs and images and the GUI will parse out the following events: 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time|Operation|
|24|Users can visualize the current state of the instrument|State Visualization|
|25|Users can scroll back in time and visualize instrument state at the various points in time|State Visualization|
|26|The application should archive the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts|Data Management|


h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process:

h3. Requirements
|| Number || Requirement || Goal ||
| | User can define missions by specifying phases | Planning |
| | User can specify and adjust phase start times | Planning |
| | User can also specify a time to wait between events instead of a specific start time | Planning |
| | User can set mission start and end times that are not associated with a phase/protocol | Planning |
| | User can specify comments associated with missions that are printed at the top of the mission script | Planning |
| | User can add non-phase/protocol events (user defined) to the calendar anywhere | Data Management |
| | User can add comments to a phase that will be generated in the script | Planning |
| |User can view images associated with phases|Data Management|
| |User can browse the .GAL file along with image and filter paper information|Data Management|
| |User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Data Management|
| |User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Data Management|
| |User can associate external files with events (excel spreadsheet, documents, etc.)|Planning,Data Mangement|
| | Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|State Visualization|
| |After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
| |Users can add/delete/edit protocol runs and phases|Planning|
| |Users can add/delete/edit consumables|Planning|
| |Application will list sample volumes with protocol run|Planning, Data Management|
| |When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown|Data Management|
| |Tide and phase information will be available|Planning,Data Management|
| |Application should allow for details of flushes to be seen/accounted for|Data Management|
| |Users can schedule Kills (end purges) or disable kills|Planning|
| |Users can define generic events and what script will actually be added to the master script (if needed)|Planning|
| |Users should be able to download instrument logs and images and the GUI will parse out the following events: 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time|Operation|
|24|Users can visualize the current state of the instrument|State Visualization|
|25|Users can scroll back in time and visualize instrument state at the various points in time|State Visualization|
|26|The application should archive the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts|Data Management|


h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
{panel}
{column}
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process:

h3. Requirements
|| Number || Requirement || Goal ||
| | User can define missions by specifying phases | Planning |
| | User can specify and adjust phase start times | Planning |
| | User can also specify a time to wait between events instead of a specific start time | Planning |
| | User can set mission start and end times that are not associated with a phase/protocol | Planning |
| | User can specify comments associated with missions that are printed at the top of the mission script | Planning |
| | User can add non-phase/protocol events (user defined) to the calendar anywhere | Data Management |
| | User can add comments to a phase that will be generated in the script | Planning |
| |User can view images associated with phases|Data Management|
| |User can browse the .GAL file along with image and filter paper information|Data Management|
| |User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Data Management|
| |User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Data Management|
| |User can associate external files with events (excel spreadsheet, documents, etc.)|Planning,Data Mangement|
| | Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|State Visualization|
| |After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
| |Users can add/delete/edit protocol runs and phases|Planning|
| |Users can add/delete/edit consumables|Planning|
| |Application will list sample volumes with protocol run|Planning, Data Management|
| |When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown|Data Management|
| |Tide and phase information will be available|Planning,Data Management|
| |Application should allow for details of flushes to be seen/accounted for|Data Management|
| |Users can schedule Kills (end purges) or disable kills|Planning|
| |Users can define generic events and what script will actually be added to the master script (if needed)|Planning|
| |Users should be able to download instrument logs and images and the GUI will parse out the following events:
* Track deployments of contextual sensors (sub-deployments of ESP)
* Collection of contextual sensor data (with capability to view/work with data) 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time|Operation|
|24|Users can visualize the current state of the instrument|State Visualization|
|25|Users can scroll back in time and visualize instrument state at the various points in time|State Visualization|
|26|The application should archive the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts|Data Management|


h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
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{column}
{section}]]></property>
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{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
# temp line, remove me, jim's try #2
{panel}
{column}
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{align}center{align}
h4. Administrative Items
{align}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
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{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
# temp line, remove me, jim's try #2
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

h4.
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
# temp line, remove me, jim's try #2
{panel}
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{panel:title=Administrative Items|borderWidth=2}
h3. {color:#009900}[ESP Logos]{color}
h2. Meeting notes
# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}

{section}
{column:width=50%}

h4. {panel:title=Engineering|borderWidth=2}

{panel}


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]
h4. System Integration
# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware
# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{column}
{column:width=50%}

h4. {panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
# temp line, remove me, jim
{panel}

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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

h4. {color:#ff00cc}Puget Sound{color}

_{+}Lummi Bay:+_

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)

*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.&nbsp; Subsequent investigation found that modem card had been cancelled with T-Mobile due to NOAA miscommunication.&nbsp; When new one was tried, operator did not know to 'close the door' on the modem in order to power the card.&nbsp; Brent flew up and fixed.&nbsp; Missed 4 days of sampling.

*August 18*\--Lummi Bay deployment ended.&nbsp; Machine returned to NOAA.

_{+}Samish Bay:&nbsp;+_

*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; No CTD.&nbsp; Both machines have MFB and PCR.&nbsp; Media event was July 18.

Aug 14--Recover Gordon

Aug 17--Deploy (swap) NEO.

Sep 10--processing syringe servo motor has failed.&nbsp; Decision to run out remaining mission with archive only.

*Sep 16*\--NEO's mission ends.&nbsp; NOAA to recover and Roman/Kevan retrieved both machines Sep 25.

h4. {color:#ff00cc}ECOHAB/CANON--Monterey Bay{color}

*&nbsp;September 10, 2013*\-\- Deploy 2 ESP's in Monterey Bay.&nbsp; First time in southern part of bay.\\

{color:#cc3366}*'North'*{color}
ESP-Mack.&nbsp; Lat 36.9048, Long \-121.93659, Water depth 32m, Can depth 9.8m.

*Oct 11, 2013*\--Battery voltage dropped too low, and we had to end mission

{color:#cc3366}*'South'*{color}
ESP-Bruce. Lat 36.63908, Long \-121.87884, Water depth 60m, Can depth 4.8m

*Oct 10, 2013*\-Found 'terminal fluid retention' on processing side-pulled an oring or some type of leak. Tried porting waste to Waste2 (known to be empty), but same results.  Final 3 samples to try and collect for SEM work.\\

*October 21, 2013* \-\- Recovered both instruments]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{panel:title=Administrative Items|borderWidth=2}
h3. {color:#009900}[ESP Logos]{color}
h2. Meeting notes
# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}

{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}
h4. &nbsp;Generation 3
# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration
# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware
# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software
# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}

{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
# temp line, remove me, jim
{panel}

{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
# temp line, remove me, jim's try #2
{panel}
{column}
{section}]]></property>
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{panel:title=h4. Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
# temp line, remove me, jim's try #2
{panel}
{column}
{section}]]></property>
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h4. {panel:title=Administrative Items|borderWidth=2}

{panel}


h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{section}
{column:width=50%}

h4. {panel:title=Engineering|borderWidth=2}

{panel}


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]
h4. System Integration
# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware
# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{column}
{column:width=50%}

h4. {panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
# temp line, remove me, jim try
{panel}

{column}
{section}]]></property>
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h4. {panel:title=Administrative Items|borderWidth=2}

{panel}


h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{section}
{column:width=50%}

h4. {panel:title=Engineering|borderWidth=2}

{panel}


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]
h4. System Integration
# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware
# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{column}
{column:width=50%}

h4. {panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
# temp line, remove me, jim
{panel}

{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://predator.shore.mbari.org/esp_gui/launch.jnlp]Project Documentation:

h3. Other Documents
# [Documents|ProjectDocuments]
# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
# [Presentations|ProjectPresentations]
# [Tasks]
# [Data Model]

h3. Bug Tracking
# [JIRA Issue Tracker|http://oceana.shore.mbari.org:8082/browse/ESPAPP]

]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [Functional Requirements for Gen 3 ESP]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Doug P, Chris S, Chris P, John R, Brent, Bill

h3. General

* &nbsp;Be sure to check out the fantastic job Kim FB is doing on the CMORE Drifter Blog.
* Kelly Lincetum from ASU may be coming out next week to go on the Zephyr and collect water.&nbsp; ASU needs 'background' and this would give them a window into foundational oceanography, and perhaps give a better appreciation of sampling issues as it relates to their PCR efforts.&nbsp; We may have a big 'filter-fest' and save some for us.

h3. ESP User Group Meeting (Sep 27-29, 2011)


* This meeting will discuss G2 items only.
* Chris S will give high-level overview.&nbsp; John R high level overview of L+O paper and BloomX update.&nbsp; Chris P high level PCR (not water quality)
* MBARI is finished at 1:30 on Tuesday, although there is an afternoon session Weds afternoon at Spyglass.&nbsp; May have Chris p, Bill, Doug attend and talk about pier stuff.
* We will suggest shortening the panel discussion Tuesday at MBARI and make room for Brent to talk about comms. (Jim to contact Spyglass)
* Also suggest moving Kevin's GUI disucussion to earlier.
* &nbsp;]]></property>
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<property name="body"><![CDATA[h1. All dates 2010


\# \[Jan 5\]]]></property>
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<property name="body"><![CDATA[h2. Opening the ESP project in an IDEA

h3. Eclipse
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# cd to the directory you checked it out to
# In a terminal run: {code}mvn eclipse:eclipse{code}
# In eclipse do _File->import_
#* Select _existing project from workspace_

h3. JBuilder
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# In Jbuilder do _File->import_
# Select _existing maven project from workspace_

h3. IntelliJ IDEA
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# cd to the directory you checked it out to
# In a terminal run: {code}mvn idea:idea{code}
# Do _File->Open Project_

h3. Netbeans
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# Install the Maven plug-in in Netbeans
## Select _Tools-Plugins_
## In the dialog that appears, select the _New Plugins_ tab
## Check the box next to *Maven*
## Press the install button
# Do _File->Open Project_
# Select the project (Netbeans will open all the child projects too)
]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}h4. Administrative Items{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h2. Opening the ESP project in an IDEA

h3. Eclipse
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# cd to the directory you checked it out to
# In a terminal run: {code}mvn eclipse:eclipse{code}
# In eclipse do _File->import_
#* Select _existing project from workspace_

h3. JBuilder
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# In Jbuilder do _File->import_
# Select _existing maven project from workspace_

h3. Netbeans
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# Install the Maven plug-in in Netbeans
## Select _Tools-Plugins_
## In the dialog that appears, select the _New Plugins_ tab
## Check the box next to *Maven*
## Press the install button
# Do _File->Open Project_
# Select the project (Netbeans will open all the child projects too)

h3. IntelliJ IDEA
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# cd to the directory you checked it out to
# In a terminal run: {code}mvn idea:idea{code}
# Do _File->Open Project_
]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}Administrative Items{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h2. Opening the ESP project in an IDEA

h3. Eclipse
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# cd to the directory you checked it out to
# In a terminal run: {code}mvn eclipse:eclipse{code}
# In eclipse do _File->import_
#* Select _existing project from workspace_

h3. JBuilder
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# In Jbuilder do _File->import_
# Select _existing maven project from workspace_

h3. Netbeans
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# Install the Maven plug-in in Netbeans
## Select _Tools-Plugins_
## In the dialog that appears, select the _New Plugins_ tab
## Check the box next to *Maven*
## Press the install button
# Do _File->Open Project_
# Select the project (Netbeans will open all the child projects too)

h3: IntelliJ IDEA
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# cd to the directory you checked it out to
# In a terminal run: {code}mvn idea:idea{code}
# Do _File->Open Project_
]]></property>
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<property name="body"><![CDATA[h2. Opening the ESP project in an IDEA

h3. Eclipse
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# cd to the directory you checked it out to
# In a terminal run: {code}mvn eclipse:eclipse{code}
# In eclipse do _File->import_
#* Select _existing project from workspace_

h3. JBuilder
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# In Jbuilder do _File->import_
# Select _existing maven project from workspace_

h3. Netbeans
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# Install the Maven plug-in in Netbeans
## Select _Tools-Plugins_
]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}h4. Administrative Items{center}
{panel|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

{note}
As of 4/1/2011, this appears to no longer work for the Mac.
{note}

h3. Prerequisites

# CVS client
# gcc
# yacc

h3. Steps to build and run

# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:
{code}
cvs checkout ESP/gen2/software
{code}
# &nbsp; (or if you want a branch like GUI2 (with head for anything not on branch \-f )
{code}
cvs checkout -f -r GUI2 ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.
{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This will populate the patch directory with the ruby source files without overwriting the patches.
# Now run configure.
{code}
./configure
{code}
# Now run make.
{code}
make
{code}
# If all goes well, ruby will have built and you can install by running this as 'root'.
{code}
make install
{code}
# After that, ruby should be ready to go and if you type
{code}
ruby --version
{code}
You should see something like:
{code}
ruby 1.6.8-mbari7/0x4770 (2009-1-19) [i686-linux]
{code}
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

h4. {color:#ff00cc}Puget Sound{color}
Lummi Bay:

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)


*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.
Samish Bay:&nbsp;
*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; Media event was July 18. ]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h4. {panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
h4. {panel:title=Engineering|borderWidth=2}




h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]
h4. System Integration
# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware
# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
h4. {panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
# temp line, remove me
{panel}

{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h4. {panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
h4. {panel:title=Engineering|borderWidth=2}




h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]
h4. System Integration
# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware
# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
h4. {panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}

{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]
# [Apr 12] \-\- Roman at WHOI, Chris P Europe
# Apr 19
# [Apr 26]
# [May 10]
# [May 17]
# May 24 \-\- Roman at WHOI, Chris S at WHOI, Chris P out
# [Jun 14] \-\- This has link to lysate dilution page
# [Jun 21]
# [Jun 28]
# Jul 5 \-\- MBARI closed
# [Jul 12] \-\- most of team at JdF
# Jul 19
# [Jul 26]
# [Aug 2]
# [Aug 9]
# Aug 16
# Aug 23
# Aug 30]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

{note}
As of 4/1/2011, this appears to no longer work for the Mac.
{note}

h3. Prerequisites

# CVS client
# gcc
# yacc

h3. Steps to build and run

# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:
{code}
cvs checkout ESP/gen2/software
{code}
# &nbsp; (or if you want a branch like GUI2 (with head for anything not on branch \-f )
{code}
cvs checkout -f -r GUI2 ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.
{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This generates a tar.gz file that contains all the source code for the ruby distribution along with the files that are custom to the MBARI use of the ruby interpreter (i.e. patches).  
# Move the ../snapshot-1.6.tar.gz file somewhere where you can expand it as this is what you will use to build the custom ruby interpreter.  
# Gunzip and untar the file (which will create a ruby directory).
# cd into the ruby directory and run configure.
{code}
./configure
{code}
# Now run make.
{code}
make
{code}
# If all goes well, ruby will have built and you can install by running this as 'root'.
{code}
make install
{code}
# After that, ruby should be ready to go and if you type
{code}
ruby --version
{code}
You should see something like:
{code}
ruby 1.6.8-mbari7/0x4770 (2009-1-19) [i686-linux]
{code}
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are four main areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "ESP and Mission Tabs Window" (lower left corner)
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|thumbnail,align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission # Shallow
# MFB
# 1km
# 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are four main areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "ESP and Mission Tabs Window" (lower left corner)
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|thumbnail,align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.

Now you can run through the [ESP GUI Quick Start Guide]
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are four main areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "ESP and Mission Tabs Window" (lower left corner)
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|thumbnail,align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are four main areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "ESP and Mission Tabs Window" (lower left corner)
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|thumbnail,align=centre!

I will describe these windows as I walk through a couple of examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
Figure 0_5
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
Figure 3
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
Figure 4
# Once you save the information, you will see your new instrument definition in the GUI.
Figure 5
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.  This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. In the following figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Figure 6
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
Figure 8
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
Figure 10
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are four main areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "ESP and Mission Tabs Window" (lower left corner)
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|thumbnail,align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">18285031</id>
<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are four main areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "ESP and Mission Tabs Window" (lower left corner)
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|thumbnail,align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">18285032</id>
<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are four main areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "ESP and Mission Tabs Window" (lower left corner)
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|thumbnail,align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission
# Shallow
# MFB
# 1km
# 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is:
{noformat}
ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700
{noformat}
which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are four main areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "ESP and Mission Tabs Window" (lower left corner)
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|thumbnail,align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission
# Shallow
# MFB
# 1km
# 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is:
{noformat}
ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700
{noformat}
which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are four main areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "ESP and Mission Tabs Window" (lower left corner)
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|thumbnail,align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission
# Shallow
# MFB
# 1km
# 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}h4. Administrative Items{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are four main areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "ESP and Mission Tabs Window" (lower left corner)
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|thumbnail,align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
Figure 12
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are four main areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "ESP and Mission Tabs Window" (lower left corner)
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|thumbnail,align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
Figure 12
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
Figure 13
# This brings up a dialog to allow you to edit specific information about this protocol run.
Figure 14
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
Figure 15
# I used the same method to add 5 more protocols to the mission plan as an example.
Figure 16
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
Figure 17
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
Figure 18.
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are four main areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "ESP and Mission Tabs Window" (lower left corner)
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|thumbnail,align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|thumbnail,align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|thumbnail,align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|thumbnail,align=centre!
# I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|thumbnail,align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|thumbnail,align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are four main areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "ESP and Mission Tabs Window" (lower left corner)
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|thumbnail,align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|thumbnail,align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|thumbnail,align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|thumbnail,align=centre!
# I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|thumbnail,align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|thumbnail,align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the ESP and Mission Tabs Window.  If you click on the "ESP" table you will see a short table with the information about the ESP that is running the mission you are examining (in this case, Gordon).
Figure 19
If you select the "Planned" tab, you will see a tabular view of the various protocols that you defined in the mission planning phase.
Figure 20
You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Samples", "Images" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates.  Which brings us to the "Files" tab.
Figure 21
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
Figure 22
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

*Dec 2, 2013*\--Fired off final sample.&nbsp; Recover slated for Dec 11, 2013. Ran a total of 24 samples, each with an archive.


h4. {color:#ff00cc}Puget Sound{color}

_{+}Lummi Bay:+_

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)

*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.&nbsp; Subsequent investigation found that modem card had been cancelled with T-Mobile due to NOAA miscommunication.&nbsp; When new one was tried, operator did not know to 'close the door' on the modem in order to power the card.&nbsp; Brent flew up and fixed.&nbsp; Missed 4 days of sampling.

*August 18*\--Lummi Bay deployment ended.&nbsp; Machine returned to NOAA.

_{+}Samish Bay:&nbsp;+_

*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; No CTD.&nbsp; Both machines have MFB and PCR.&nbsp; Media event was July 18.

Aug 14--Recover Gordon

Aug 17--Deploy (swap) NEO.

Sep 10--processing syringe servo motor has failed.&nbsp; Decision to run out remaining mission with archive only.

*Sep 16*\--NEO's mission ends.&nbsp; NOAA to recover and Roman/Kevan retrieved both machines Sep 25.

h4. {color:#ff00cc}ECOHAB/CANON--Monterey Bay{color}

*&nbsp;September 10, 2013*\-\- Deploy 2 ESP's in Monterey Bay.&nbsp; First time in southern part of bay.
\\

{color:#cc3366}*'North'*{color}
ESP-Mack.&nbsp; Lat 36.9048, Long \-121.93659, Water depth 32m, Can depth 9.8m.

*Oct 11, 2013*\--Battery voltage dropped too low, and we had to end mission

{color:#cc3366}*'South'*{color}
ESP-Bruce. Lat 36.63908, Long \-121.87884, Water depth 60m, Can depth 4.8m

*Oct 10, 2013*\-Found 'terminal fluid retention' on processing side-pulled an oring or some type of leak. Tried porting waste to Waste2 (known to be empty), but same results.  Final 3 samples to try and collect for SEM work.
\\

*October 21, 2013* \-\- Recovered both instruments]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

Figure 1

There are four main areas in the ESP GUI:
# The instrument list window (upper left corner)
# The calendar window (upper right corner)
# The ESP and Mission tabs (lower left corner)
# The context sensitive details pane (lower right corner).

Figure 2

I will describe these windows as I walk through a couple of examples.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
Figure 3
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note|title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
Figure 4]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application.]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
# Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
## Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
## Or you should be able to double click on the jar in most cases.
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.
{noformat}
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost'
    ->     WITH GRANT OPTION;
{noformat}
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
### Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

Figure 1

There are four main areas in the ESP GUI:
# The instrument list window (upper left corner)
# The calendar window (upper right corner)
# The ESP and Mission tabs (lower left corner)
# The context sensitive details pane (lower right corner).

Figure 2

I will describe these windows as I walk through a couple of examples.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
Figure 3
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
Figure 4
# Once you save the information, you will see your new instrument definition in the GUI.
Figure 5
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.  This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. In the following figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Figure 6
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

Figure 1

There are four main areas in the ESP GUI:
# The instrument list window (upper left corner)
# The calendar window (upper right corner)
# The ESP and Mission tabs (lower left corner)
# The context sensitive details pane (lower right corner).

Figure 2

I will describe these windows as I walk through a couple of examples.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
Figure 3
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
Figure 4
# Once you save the information, you will see your new instrument definition in the GUI.
Figure 5
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.  This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. In the following figure, we have defined a new protocol with the name 'HAB' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 1000ml as well.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 120 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to be run).
Figure 6
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'hab' (not case sensitive so 'HAB' or 'HaB' is fine too).
{note}]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are four main areas in the ESP GUI:
# The instrument list window (upper left corner)
# The calendar window (upper right corner)
# The ESP and Mission tabs (lower left corner)
# The context sensitive details pane (lower right corner).

Figure 2

I will describe these windows as I walk through a couple of examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
Figure 0_5
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
Figure 3
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
Figure 4
# Once you save the information, you will see your new instrument definition in the GUI.
Figure 5
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.  This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. In the following figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Figure 6
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
Figure 8
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
Figure 10
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

Figure 1

There are four main areas in the ESP GUI:
# The instrument list window (upper left corner)
# The calendar window (upper right corner)
# The ESP and Mission tabs (lower left corner)
# The context sensitive details pane (lower right corner).

Figure 2

I will describe these windows as I walk through a couple of examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
Figure 0_5
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
Figure 3
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
Figure 4
# Once you save the information, you will see your new instrument definition in the GUI.
Figure 5
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.  This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. In the following figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Figure 6
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
Figure 8
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
Figure 10
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

Figure 1

There are four main areas in the ESP GUI:
# The instrument list window (upper left corner)
# The calendar window (upper right corner)
# The ESP and Mission tabs (lower left corner)
# The context sensitive details pane (lower right corner).

Figure 2

I will describe these windows as I walk through a couple of examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
Figure 0_5
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _Juan De Fuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/Juan De Fuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "Juan De Fuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/Juan De Fuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
Figure 3
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
Figure 4
# Once you save the information, you will see your new instrument definition in the GUI.
Figure 5
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.  This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. In the following figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Figure 6
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
Figure 8
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
Figure 10
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _Juan De Fuca_ |]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

Figure 1

There are four main areas in the ESP GUI:
# The instrument list window (upper left corner)
# The calendar window (upper right corner)
# The ESP and Mission tabs (lower left corner)
# The context sensitive details pane (lower right corner).

Figure 2

I will describe these windows as I walk through a couple of examples.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
Figure 3
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
Figure 4]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

Figure 1

There are four main areas in the ESP GUI:
# The instrument list window (upper left corner)
# The calendar window (upper right corner)
# The ESP and Mission tabs (lower left corner)
# The context sensitive details pane (lower right corner).

Figure 2

I will describe these windows as I walk through a couple of examples.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
Figure 3
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
Figure 4
# Once you save the information, you will see your new instrument definition in the GUI.
Figure 5
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.  This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. In the following figure, we have defined a new protocol with the name 'HAB' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 1000ml as well.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 120 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to be run).
Figure 6
# This brings up a ]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

Figure 1

There are four main areas in the ESP GUI:
# The instrument list window (upper left corner)
# The calendar window (upper right corner)
# The ESP and Mission tabs (lower left corner)
# The context sensitive details pane (lower right corner).

Figure 2

I will describe these windows as I walk through a couple of examples.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
Figure 3
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
Figure 4
# Once you save the information, you will see your new instrument definition in the GUI.
Figure 5
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
\\
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage taken by Rob Vincent:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]

Map of locations:&nbsp; [http://maps.google.com/maps/ms?ie=UTF&msa=0&msid=213220825771739778963.0004a40bdd601babc291d]

May 23.&nbsp; Attempted recovery of ESP.&nbsp; Message from Roman:

{color:#996600}&nbsp;&nbsp;&nbsp; We went out to the site where espbruce was moored and attempted to find it.&nbsp; The weather was very poor and water was very turbid.&nbsp; Using the ships depth finder we found a promising target.&nbsp; In difficult conditions the divers performed a search but espbruce was not found.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; We recovered the mooring.&nbsp; It looks like the cable was pulled straight out of the cone.&nbsp; The top mast is bent but I cannot say if this was caused by a rough landing on the beach or boat impact.&nbsp; There are no dents or gouges on the mooring.&nbsp; The radio box is dry and antenna looks ok.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; Thursday the RV Gulf Challenger may be able to survey the area with a side scanning sonar.&nbsp; This will be a much better way to search for espbruce.&nbsp;{color}

Message from Roman May 26:

{color:#996600}&nbsp;&nbsp;&nbsp; ESPbruce was located at&nbsp; 43° 02.0740 N&nbsp;&nbsp; 70° 36.8447 W at ~ 10m depth.&nbsp; This position is about 19 yards from the waypoint.&nbsp; So looks like it wasn't dragged and has maintained seal integrity.&nbsp; We will attempt to recover it this weekend if we can get the RV Tioga.&nbsp; If not will recover with the RV Connecticut on june 7th weather permitting.{color}
&nbsp;

Dates for a recovery kept moving as weather and scheduling problems arose.&nbsp; Finally, Roman reported on June 15:
{quote}
{quote}
{color:#996600}ESPbruce was recovered today with no visible external damage. The EM cable strain relief is still on the cable.&nbsp; The recovery operation used two ships the RV Gulf Challenger and it's sister the RV Tioga.&nbsp; The Challenger supported the the side scan survey and the Tioga supported the divers and lifting of the core package and its anchor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;The side scan sonar operator advised me at the beginning of the day that he believed the esp package would be found on the bottom.&nbsp; He based this opinion on the data secured by his colleague almost two weeks ago.&nbsp; From his read of that run, he believed that the instrument was 15m off the bottom at that time.&nbsp; Depth at this site is 49m.&nbsp; He felt that the instrument was slowly sinking and that by today it was surly be on the sea floor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Todays side scan survey took approximately 90 minutes.&nbsp; They had acquired a strong signature on the core and calculated that it was at a depth of 65 feet (~20m). The package&nbsp; was still located within 10m of the original deployment site.&nbsp; They dropped a marker line with a float as close to the calculated position as possible.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;At this point divers equipped with twin 80 cu ft Nitrox cylinders and electric scooters dived on the marker.&nbsp; They had 70 minutes of search time.&nbsp; After 42 minutes an orange sausage float attached to a spectra lift line appeared.&nbsp; Then 10 minutes later a second lift bag attached to the EM cable appeared.&nbsp; The divers surfaced after a total bottom time of 62 minutes.&nbsp; Eight minutes to spare.&nbsp; We recovered the divers.&nbsp; They reported that the depth of top of the can was at 26 feet (~8m) right where it was supposed to be.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Recovery went smoothly using a single winch equipped with a capstan attachment.&nbsp; By alternately shifting the load from drum (used to lift anchor) and capstan (used to lift instrument we recovered the package and the anchor safely.{color}
{quote}
\\
\\  {color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford.

{color:#cc3300}July 6{color} \-\- Ship by truck D-ESP and supplies for JdF cruise.&nbsp; To Newport, OR. ]]></property>
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<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically (colors are same deployment)+

{color:#ff00ff}April 6--Bruce at M0 for surface deployment (Zephyr){color}

April 15--Mack in Sphere (dive #1) for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in Sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

{color:#ff00ff}April 29--Recover Bruce at M0 (Zephyr){color}

May 1--Mack in Sphere (dive #3) connected to DWSM; incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

{color:#0033cc}May 14--Deploy NEO w/PCR, surface deployment (Zephyr){color}

May 27--First Drifter dive; used weighted cable (Zephyr)

June 5-9 \-\- Western Flyer Trip.&nbsp; D-ESP, Drifter, and CTD casts. {color:#cc0000}{*}MOVIES{*}{color}:  D-ESP launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/DESP%20deployment%20(full%20quality).dv].  Drifter launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/Drifter.dv].

{color:#0033cc}June 11 \-\- Recover NEO.&nbsp; (Zephyr){color}\\

+FALL Network Deployment+

Proposed locations are here: [http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&msid=113879459163411006053.000471828af997bd7d89c&t=h&z=12]

{color:#ff6600}September 24 \-\- Deploy Moe w/PCR at M0.&nbsp; Deployed Mack at Santa Cruz{color}.&nbsp; {color:#66cc00}Deployed Bruce in the bight.&nbsp; (Zephyr)&nbsp; Lost communications with Bruce that day.{color}

{color:#66cc00}September 28 \-\- Recover (dead) Bruce.&nbsp; Comms box had water in it, but radio worked.&nbsp; EM cable had 2 broken wires. (Zephyr){color}

{color:#cc0000}September 30 \-\- Deploy D-ESP on MARS (Lobos).{color}&nbsp; Hand issue at first, but 'fixed' itself.&nbsp; Worked until Oct. 7 when wrong puck was loaded and water introduced into core, frying puck heater.&nbsp; We turned off and first recovery day (Oct 13) is weathered out.&nbsp; It still awaits recovery.

{color:#66cc00}October 14 \-\- Re-deploy Bruce (Zephyr).&nbsp; New comms box, re-terminated EM cable.&nbsp; Working well after deployment.{color}

October 20 \-\- Install pump system on pier at Santa Cruz Wharf. October 22 \-\- Neo installed on SC Wharf.

{color:#cc0000}October 30 \-\- Recover D-ESP off MARS (Lobos).{color}

{color:#ff6600}October 29 \-\- Recover both Moe from M0 and Mack from Santa Cruz (Zephyr).{color}

{color:#66cc00}November 2 \-\- Recover Bruce from the bight (Zephyr).&nbsp; This ends Fall Network Deployment.{color}

November 25 \-\- Recover NEO from SC Wharf.

{color:#ff00ff}December 14 \-\- Deploy D-ESP (Gordon) on MARS (Lobos).{color} ]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [Functional Requirements for Gen 3 ESP]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h4. {panel:title=Administrative Items|borderWidth=2}




h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]
{panel}

{section}
{column:width=50%}

h4. {panel:title=Engineering|borderWidth=2}




h4. &nbsp;Generation 3

### [Requirements]
### [Detection Technologies]
### [Functional Requirements for Gen 3 ESP]
### [Development Leads]
h4. System Integration
### [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
### [Engineering Timeline] 2008
### [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
### [Cheat Sheet]
### [Container Storage Locker Information (10-1-2008)]
h4. Hardware
### [Deep ESP]
### [Melo Iridium Tracker]
### [Micro-Fluidics Block]
### [LLNL PCR heater module]
### [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
### [Sampling Wand Functional Req's] \- NEW -
### [DWSM--4k Deep Water Sampling Module]
### [Puck Numbering System]
### [Frit Identification system]
### [ISUS issues] (updated 31 Aug 2010)

h4. Software

### [Instrument Software Revision Level]
### [JIRA Bug Tracker|https://oceana.mbari.org/jira]
### [GUI Component Development Pages|2G ESP GUI Application]
### [ESP Image Analysis Application]
### [Power Commands (9-30-08)]
### [Radio Communication commands for tri-deployment (10-7-08)]
### [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
### [How To Get the ESP Software Running On Your Machine]
### [CVS For McLane]
### [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}

h4. {panel:title=Science|borderWidth=2}
### [2008 Deployments]
### [2009 Deployments]
### [2010 Deployments]
### [2011 Deployments]
#### [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
### [MFB-PCR distribution list] as of 4Nov2010
{panel}

{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h4. {panel:title=Administrative Items|borderWidth=2}

{panel}


h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{section}
{column:width=50%}

h4. {panel:title=Engineering|borderWidth=2}

{panel}


h4. &nbsp;Generation 3

### [Requirements]
### [Detection Technologies]
### [Functional Requirements for Gen 3 ESP]
### [Development Leads]
h4. System Integration
### [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
### [Engineering Timeline] 2008
### [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
### [Cheat Sheet]
### [Container Storage Locker Information (10-1-2008)]
h4. Hardware
### [Deep ESP]
### [Melo Iridium Tracker]
### [Micro-Fluidics Block]
### [LLNL PCR heater module]
### [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
### [Sampling Wand Functional Req's] \- NEW -
### [DWSM--4k Deep Water Sampling Module]
### [Puck Numbering System]
### [Frit Identification system]
### [ISUS issues] (updated 31 Aug 2010)

h4. Software

### [Instrument Software Revision Level]
### [JIRA Bug Tracker|https://oceana.mbari.org/jira]
### [GUI Component Development Pages|2G ESP GUI Application]
### [ESP Image Analysis Application]
### [Power Commands (9-30-08)]
### [Radio Communication commands for tri-deployment (10-7-08)]
### [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
### [How To Get the ESP Software Running On Your Machine]
### [CVS For McLane]
### [Helpful DEBUGGING commands to discern machine state]
{column}
{column:width=50%}

h4. {panel:title=Science|borderWidth=2}
### [2008 Deployments]
### [2009 Deployments]
### [2010 Deployments]
### [2011 Deployments]
#### [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
### [MFB-PCR distribution list] as of 4Nov2010
{panel}

{column}
{section}]]></property>
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<property name="body"><![CDATA[\\
{tip:title=Who we purchased from:}

h2. American Portable Storage

Oakland, CA
1-800-838-4006&nbsp;&nbsp; &nbsp;(Ken)

+Rental Information+
220V single phase (newer; quiet)
Delivery/pickup $850
$650/mo w/ 2 mo min.&nbsp; Uses $95/mo electricity.

220V 3-phase
$600/mo.&nbsp; Older noisy.&nbsp; Uses $450/mo electricity.

{color:#ff0000}UPDATE on our{color} {color:#ff0000}{_}{+}purchase{+}{_}{color} {color:#ff0000}(2-25-2009){color}

Purchased 20' van, 220V Single Phase with 3hp refrigeration system, good from \-10 to 55F.&nbsp; SS sides, aluminum floor.
Michael McCurley--his quote is [here|^MBARI Quote.doc].
Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].
PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)
{tip}

h2. Aztec Containers

Stockton, CA
1-800-399-2126 (Mark)

220 3-phase
Delivery/pickup $495
$695/mo w/ 3 mo min.

h2. Refrigerated Container Services

Oakland, CA
1-510-568-9541

220 3-phase
delivery/pickup \~$500
$1000/mo w/ no minimum.

Could purchase for \~$7800.&nbsp; They may repurchase for ½ price after we're finished.

Reefers only have doors on one end.&nbsp; No lights.&nbsp; Pass-throughs?&nbsp; Unknown.]]></property>
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<property name="body"><![CDATA[\\
{tip:title=Who we purchased the D-ESP van from:}

h2. American Portable Storage

Oakland, CA
1-800-838-4006&nbsp;&nbsp; &nbsp;(Ken)

+Rental Information+
220V single phase (newer; quiet)
Delivery/pickup $850
$650/mo w/ 2 mo min.&nbsp; Uses $95/mo electricity.

220V 3-phase
$600/mo.&nbsp; Older noisy.&nbsp; Uses $450/mo electricity.

{color:#ff0000}UPDATE on our{color} {color:#ff0000}{_}{+}purchase{+}{_}{color} {color:#ff0000}(2-25-2009){color}

Purchased 20' van, 220V Single Phase with 3hp refrigeration system, good from \-10 to 55F.&nbsp; SS sides, aluminum floor.
Michael McCurley--his quote is [here|^MBARI Quote.doc].
Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].
PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)
{tip}

h2. Aztec Containers

Stockton, CA
1-800-399-2126 (Mark)

220 3-phase
Delivery/pickup $495
$695/mo w/ 3 mo min.

h2. Refrigerated Container Services

Oakland, CA
1-510-568-9541

220 3-phase
delivery/pickup \~$500
$1000/mo w/ no minimum.

Could purchase for \~$7800.&nbsp; They may repurchase for ½ price after we're finished.

Reefers only have doors on one end.&nbsp; No lights.&nbsp; Pass-throughs?&nbsp; Unknown.]]></property>
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<property name="body"><![CDATA[\\
{tip:title=Who we purchased the D-ESP van from:}

h2. American Portable Storage

Oakland, CA
1-800-838-4006; &nbsp;(Ken)

+Rental Information+
220V single phase (newer; quiet)
Delivery/pickup $850
$650/mo w/ 2 mo min.&nbsp; Uses $95/mo electricity.

220V 3-phase
$600/mo.&nbsp; Older noisy.&nbsp; Uses $450/mo electricity.

{color:#ff0000}UPDATE on our{color} {color:#ff0000}{_}{+}purchase{+}{_}{color} {color:#ff0000}(2-25-2009){color}

Purchased 20' van, 220V Single Phase with 3hp refrigeration system, good from \-10 to 55F.&nbsp; SS sides, aluminum floor.
Michael McCurley--his quote is [here|^MBARI Quote.doc].
Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].
PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)
{tip}


{tip:title=Who we purchased the Reefer Shipping Van from:}

h2.  Cold Box  (I believe this was a spin-off of APS above)

Oakland, CA
1-800-595-0601; (Mario Leon)

Quote is [here|^Shipping Van quote.pdf]

PO is [here|^Shipping Van PO.pdf]

{tip}
]]></property>
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<property name="body"><![CDATA[\\
{tip:title=Who we purchased the D-ESP van from:}

h2. American Portable Storage

Oakland, CA
1-800-838-4006; &nbsp;(Ken)

+Rental Information+
220V single phase (newer; quiet)
Delivery/pickup $850
$650/mo w/ 2 mo min.&nbsp; Uses $95/mo electricity.

220V 3-phase
$600/mo.&nbsp; Older noisy.&nbsp; Uses $450/mo electricity.

{color:#ff0000}UPDATE on our{color} {color:#ff0000}{_}{+}purchase{+}{_}{color} {color:#ff0000}(2-25-2009){color}

Purchased 20' van, 220V Single Phase with 3hp refrigeration system, good from \-10 to 55F.&nbsp; SS sides, aluminum floor.
Michael McCurley--his quote is [here|^MBARI Quote.doc].
Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].
PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)
{tip}

h2. Aztec Containers

Stockton, CA
1-800-399-2126 (Mark)

220 3-phase
Delivery/pickup $495
$695/mo w/ 3 mo min.

h2. Refrigerated Container Services

Oakland, CA
1-510-568-9541

220 3-phase
delivery/pickup \~$500
$1000/mo w/ no minimum.

Could purchase for \~$7800.&nbsp; They may repurchase for ½ price after we're finished.

Reefers only have doors on one end.&nbsp; No lights.&nbsp; Pass-throughs?&nbsp; Unknown.]]></property>
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<property name="body"><![CDATA[\\
{tip:title=Who we purchased the D-ESP van from:}

h2. American Portable Storage

Oakland, CA
1-800-838-4006; &nbsp;(Ken)

+Rental Information+
220V single phase (newer; quiet)
Delivery/pickup $850
$650/mo w/ 2 mo min.&nbsp; Uses $95/mo electricity.

220V 3-phase
$600/mo.&nbsp; Older noisy.&nbsp; Uses $450/mo electricity.

{color:#ff0000}UPDATE on our{color} {color:#ff0000}{_}{+}purchase{+}{_}{color} {color:#ff0000}(2-25-2009){color}

Purchased 20' van, 220V Single Phase with 3hp refrigeration system, good from \-10 to 55F.&nbsp; SS sides, aluminum floor.
Michael McCurley--his quote is [here|^MBARI Quote.doc].
Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].
PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)
{tip}
{tip:title=Who we purchased the Reefer Shipping Van from:}

h2. Cold Box  (I believe this was a spin-off of APS above)

Oakland, CA
1-800-595-0601; (Mario Leon)

Quote is [here|^Shipping Van quote.pdf]

PO is [here|^Shipping Van PO.pdf]
{tip}]]></property>
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<property name="body"><![CDATA[\\
{tip:title=Who we purchased the D-ESP van from:}

h2. American Portable Storage

Purchased Feb, 2009

Oakland, CA
1-800-838-4006; &nbsp;(Ken)

Purchased 20' van, 220V Single Phase with 3hp refrigeration system, good from \-10 to 55F.&nbsp; SS sides, aluminum floor.
Michael McCurley--his quote is [here|^MBARI Quote.doc].
Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].
PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)
{tip}
{tip:title=Who we purchased the Reefer Shipping Van from:}

h2. Cold Box  (I believe this was a spin-off of APS above)

Purchased July, 2011

Oakland, CA
1-800-595-0601; (Mario Leon)Quote is [here|^Shipping Van quote.pdf]

PO is [here|^Shipping Van PO.pdf]
{tip}]]></property>
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<property name="body"><![CDATA[\\
{tip:title=Who we purchased the D-ESP van from:}

h2. American Portable Storage

Purchased Feb, 2009


Oakland, CA
1-800-838-4006; &nbsp;(Ken)

Purchased 20' van, 220V Single Phase with 3hp refrigeration system, good from \-10 to 55F.&nbsp; SS sides, aluminum floor.
Michael McCurley--his quote is [here|^MBARI Quote.doc].
Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].
PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)
{tip}
{tip:title=Who we purchased the Reefer Shipping Van from:}

h2. Cold Box  (I believe this was a spin-off of APS above)

Purchased July, 2011


Oakland, CA
1-800-595-0601; (Mario Leon)

Quote is [here|^Shipping Van quote.pdf]

PO is [here|^Shipping Van PO.pdf]
{tip}]]></property>
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<property name="body"><![CDATA[\\
{tip:title=Who we purchased the D-ESP van from:}

h2. American Portable Storage

Purchased Feb, 2009

Oakland, CA
1-800-838-4006; &nbsp;(Ken)

Purchased 20' van, 220V Single Phase with 3hp refrigeration system, good from \-10 to 55F.&nbsp; SS sides, aluminum floor.
Michael McCurley--his quote is [here|^MBARI Quote.doc].
Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].
PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)
{tip}
{tip:title=Who we purchased the Reefer Shipping Van from:}

h2. Cold Box  (I believe this was a spin-off of APS above)
Purchased July, 2011
Oakland, CA
1-800-595-0601; (Mario Leon)
Quote is [here|^Shipping Van quote.pdf]
PO is [here|^Shipping Van PO.pdf]
{tip}]]></property>
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{tip:title=Who we purchased the D-ESP van from:}

h2. American Portable Storage

Purchased Feb, 2009

Oakland, CA
1-800-838-4006; &nbsp;(Ken)

Purchased 20' van, 220V Single Phase with 3hp refrigeration system, good from \-10 to 55F.&nbsp; SS sides, aluminum floor.
Michael McCurley--his quote is [here|^MBARI Quote.doc].
Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].
PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)
{tip}
{tip:title=Who we purchased the Reefer Shipping Van from:}

h2. Cold Box  (I believe this was a spin-off of APS above)

Purchased July, 2011

Oakland, CA
1-800-595-0601; (Mario Leon)
Quote is [here|^Shipping Van quote.pdf]
PO is [here|^Shipping Van PO.pdf]
{tip}]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]
# [Apr 12] \-\- Roman at WHOI, Chris P Europe
# Apr 19
# [Apr 26]
# [May 10]
# [May 17]
# May 24 \-\- Roman at WHOI, Chris S at WHOI, Chris P out
# [Jun 14] \-\- This has link to lysate dilution page
# [Jun 21]
# [Jun 28]
# Jul 5 \-\- MBARI closed
# [Jul 12] \-\- most of team at JdF
# Jul 19
# [Jul 26]]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] \- first discussion of adaptive sampling strategies
# Mar 3 - CMORE Hawaii
# [Mar 10] \-\- wand schematic
# [Mar 17]
# [Mar 24]
# Mar 31 - team deploying MOE at M0; Brent at WHOI
# [Apr 7]
# [Apr 14]
# [Apr 21]\--wand schematic reminder...
# [Apr 28]\--D-ESP 2-Year Birthday Celebration\!\!&nbsp; (Poster is [here|^ESP Birthday Poster(smaller).pdf])
# May 5 \-\- Visit to ASU
# [May 12]
# [May 19]
# [May 26]
# [Jun 2]
# Jun 9
# Jun 16
# [Jun 23]
# [Jun 30] \--Final prep before JdF]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]
# [Apr 12] \-\- Roman at WHOI, Chris P Europe
# Apr 19
# [Apr 26]
# [May 10]
# [May 17]
# May 24 \-\- Roman at WHOI, Chris S at WHOI, Chris P out
# [Jun 14] \-\- This has link to lysate dilution page
# [Jun 21]
# [Jun 28]
# Jul 5 \-\- MBARI closed
# [Jul 12] \-\- most of team at JdF
# Jul 19
# [Jul 26]
# Aug 2
# Aug 9
# Aug 16
# Aug 23
# Aug 30
]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] \- first discussion of adaptive sampling strategies
# Mar 3 - CMORE Hawaii
# [Mar 10] \-\- wand schematic
# [Mar 17]
# [Mar 24]
# Mar 31 - team deploying MOE at M0; Brent at WHOI
# [Apr 7]
# [Apr 14]
# [Apr 21]\--wand schematic reminder...
# [Apr 28]\--D-ESP 2-Year Birthday Celebration\!\!&nbsp; (Poster is [here|^ESP Birthday Poster(smaller).pdf])
# May 5 \-\- Visit to ASU
# [May 12]
# [May 19]
# [May 26]
# [Jun 2]
# Jun 9
# Jun 16
# [Jun 23]
# [Jun 30] \--Final prep before JdF
# Jul 7
# Jul 14
# Jul 21
# Jul 28
# Aug 4
# Aug 11
# Aug 18
# Aug 25
# Sep 1
]]></property>
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<property name="body"><![CDATA[\\

h2. \\


h2.


h2.


h2. Discussion of Drifter Issues
\\
# Will send MELO notifications to jrobidart@gmail.com and to esp001@mbari.org
# Sea-test on Aug 11 on Shana Rae.&nbsp; (This subsequently got moved to Aug 12).
# Working in van will require constant hearing protection
# Travel.&nbsp; EVERYTHING goes through Annette.&nbsp; Deployment will be charged to 708602.05\\]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]
# [Apr 12] \-\- Roman at WHOI, Chris P Europe
# Apr 19
# [Apr 26]
# [May 10]
# [May 17]
# May 24 \-\- Roman at WHOI, Chris S at WHOI, Chris P out
# [Jun 14] \-\- This has link to lysate dilution page
# [Jun 21]
# [Jun 28]
# Jul 5 \-\- MBARI closed
# [Jul 12] \-\- most of team at JdF
# Jul 19
# [Jul 26]
# [Aug 2]
# Aug 9
# Aug 16
# Aug 23
# Aug 30]]></property>
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<property name="body"><![CDATA[\\
{tip:title=Who we purchased the D-ESP van from:}

h2. American Portable Storage

Purchased Feb, 2009
Oakland, CA
1-800-838-4006; &nbsp;(Ken)

Purchased 20' van, 220V Single Phase with 3hp refrigeration system, good from \-10 to 55F.&nbsp; SS sides, aluminum floor.
Michael McCurley--his quote is [here|^MBARI Quote.doc].
Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].
PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)
{tip}
{tip:title=Who we purchased the Reefer Shipping Van from:}

h2. Cold Box  (I believe this was a spin-off of APS above)

Purchased July, 2011
Oakland, CA
1-800-595-0601; (Mario Leon)
Quote is [here|^Shipping Van quote.pdf]
PO is [here|^Shipping Van PO.pdf]
{tip}]]></property>
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<property name="body"><![CDATA[Our first 'labeled' scintered frits arrived *{+}23 April, 2008{+}*.&nbsp; These were 10um frits, labeled 'D'. Specifics of this order:

Job #36366
Disc Dimensions: 0.998 \+0.000/-0.002" OD x 0.062 \+/-0.005" thick
Porous Grade: 10 Micron Grade
No Chamfers
Porous material Chemistry: Titanium Grade 2 per unified
PO# 0810358&nbsp;

These frits did {color:#cc0000}NOT{color} have finished edges, and were 0.057" in thickness, within tolerance specified, but thinner than original frits.
Future orders should specify edging and a lower thickness tolerance to get closer to the 0.062" thickness.
\\

The convention, decided in emails Feb 26, 2008, will be:

0.1, 0.5, 1, 10um frits will be labeled

A, B, C, D respectively.&nbsp;
\\

We have had CE Metallurgical make the 'press' for these so subsequent batches should be less expensive.&nbsp;

*{+}March 26, 2009{+}*

Jobs #38015, 38016, 38017
Disc Dimensions: 0.998 \+0.000/-0.002 OD x 0.063 \+/-0.003" thick&nbsp; (note slightly thicker with narrower tolerance than first order)
PO# 0910403

0.1 um (labeld 'A') $10.25/ea
20.0 um (labeled 'E') $7.55/ea
50.0 um (labeled 'F') $7.55/ea

Ordered 100 of each size.

*+&nbsp;December 30, 2009{+}*

Placed the following order:

Jobs
Disc Dimensions: 0.998 \+0.000/-0.002 OD x 0.063 \+/-0.003" thick
PO

0.2 um (100; labeled '2') $10.25/ea
0.5 um (100; labeled 'B') $10.25/ea
1.0 um (100; labeled 'C') $10.25/ea
10 um (300; labeled 'D') $5.85/ea

{color:#0000ff}Contact{color}:

Chand Eisenmann Metallurgical
258 Spielman Hwy
Burlington, CT&nbsp; 06013

860-675-5000

{color:#0000ff}email:{color}
me@chandeisenmann.com&nbsp; (Mark Eisenmann)]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
\\
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage taken by Rob Vincent:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]

Map of locations:&nbsp; [http://maps.google.com/maps/ms?ie=UTF&msa=0&msid=213220825771739778963.0004a40bdd601babc291d]

May 23.&nbsp; Attempted recovery of ESP.&nbsp; Message from Roman:

{color:#996600}&nbsp;&nbsp;&nbsp; We went out to the site where espbruce was moored and attempted to find it.&nbsp; The weather was very poor and water was very turbid.&nbsp; Using the ships depth finder we found a promising target.&nbsp; In difficult conditions the divers performed a search but espbruce was not found.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; We recovered the mooring.&nbsp; It looks like the cable was pulled straight out of the cone.&nbsp; The top mast is bent but I cannot say if this was caused by a rough landing on the beach or boat impact.&nbsp; There are no dents or gouges on the mooring.&nbsp; The radio box is dry and antenna looks ok.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; Thursday the RV Gulf Challenger may be able to survey the area with a side scanning sonar.&nbsp; This will be a much better way to search for espbruce.&nbsp;{color}

Message from Roman May 26:

{color:#996600}&nbsp;&nbsp;&nbsp; ESPbruce was located at&nbsp; 43° 02.0740 N&nbsp;&nbsp; 70° 36.8447 W at ~ 10m depth.&nbsp; This position is about 19 yards from the waypoint.&nbsp; So looks like it wasn't dragged and has maintained seal integrity.&nbsp; We will attempt to recover it this weekend if we can get the RV Tioga.&nbsp; If not will recover with the RV Connecticut on june 7th weather permitting.{color}
&nbsp;

Dates for a recovery kept moving as weather and scheduling problems arose.&nbsp; Finally, Roman reported on June 15:
{quote}
{quote}
{color:#996600}ESPbruce was recovered today with no visible external damage. The EM cable strain relief is still on the cable.&nbsp; The recovery operation used two ships the RV Gulf Challenger and it's sister the RV Tioga.&nbsp; The Challenger supported the the side scan survey and the Tioga supported the divers and lifting of the core package and its anchor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;The side scan sonar operator advised me at the beginning of the day that he believed the esp package would be found on the bottom.&nbsp; He based this opinion on the data secured by his colleague almost two weeks ago.&nbsp; From his read of that run, he believed that the instrument was 15m off the bottom at that time.&nbsp; Depth at this site is 49m.&nbsp; He felt that the instrument was slowly sinking and that by today it was surly be on the sea floor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Todays side scan survey took approximately 90 minutes.&nbsp; They had acquired a strong signature on the core and calculated that it was at a depth of 65 feet (~20m). The package&nbsp; was still located within 10m of the original deployment site.&nbsp; They dropped a marker line with a float as close to the calculated position as possible.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;At this point divers equipped with twin 80 cu ft Nitrox cylinders and electric scooters dived on the marker.&nbsp; They had 70 minutes of search time.&nbsp; After 42 minutes an orange sausage float attached to a spectra lift line appeared.&nbsp; Then 10 minutes later a second lift bag attached to the EM cable appeared.&nbsp; The divers surfaced after a total bottom time of 62 minutes.&nbsp; Eight minutes to spare.&nbsp; We recovered the divers.&nbsp; They reported that the depth of top of the can was at 26 feet (~8m) right where it was supposed to be.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Recovery went smoothly using a single winch equipped with a capstan attachment.&nbsp; By alternately shifting the load from drum (used to lift anchor) and capstan (used to lift instrument we recovered the package and the anchor safely.{color}
{quote}
\\
\\  {color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford.

{color:#cc3300}July 6{color} \-\- Ship by truck D-ESP and supplies for JdF cruise.&nbsp; To Newport, OR.

{color:#cc3300}July 13{color} \-\- Sail for Axial and JdF (1 day late due to weather getting up to Newport)

{color:#cc0000}July 20{color} \-\- recall D-ESP.&nbsp; Recover all instruments.&nbsp; Two more days for Dave Clague.&nbsp; Ship returns July 23. ]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]
# [May 20]]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
\\
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage taken by Rob Vincent:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]

Map of locations:&nbsp; [http://maps.google.com/maps/ms?ie=UTF&msa=0&msid=213220825771739778963.0004a40bdd601babc291d]

May 23.&nbsp; Attempted recovery of ESP.&nbsp; Message from Roman:

{color:#996600}&nbsp;&nbsp;&nbsp; We went out to the site where espbruce was moored and attempted to find it.&nbsp; The weather was very poor and water was very turbid.&nbsp; Using the ships depth finder we found a promising target.&nbsp; In difficult conditions the divers performed a search but espbruce was not found.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; We recovered the mooring.&nbsp; It looks like the cable was pulled straight out of the cone.&nbsp; The top mast is bent but I cannot say if this was caused by a rough landing on the beach or boat impact.&nbsp; There are no dents or gouges on the mooring.&nbsp; The radio box is dry and antenna looks ok.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; Thursday the RV Gulf Challenger may be able to survey the area with a side scanning sonar.&nbsp; This will be a much better way to search for espbruce.&nbsp;{color}

Message from Roman May 26:

{color:#996600}&nbsp;&nbsp;&nbsp; ESPbruce was located at&nbsp; 43° 02.0740 N&nbsp;&nbsp; 70° 36.8447 W at ~ 10m depth.&nbsp; This position is about 19 yards from the waypoint.&nbsp; So looks like it wasn't dragged and has maintained seal integrity.&nbsp; We will attempt to recover it this weekend if we can get the RV Tioga.&nbsp; If not will recover with the RV Connecticut on june 7th weather permitting.{color}
&nbsp;

Dates for a recovery kept moving as weather and scheduling problems arose.&nbsp; Finally, Roman reported on June 15:
{quote}
{quote}
{color:#996600}ESPbruce was recovered today with no visible external damage. The EM cable strain relief is still on the cable.&nbsp; The recovery operation used two ships the RV Gulf Challenger and it's sister the RV Tioga.&nbsp; The Challenger supported the the side scan survey and the Tioga supported the divers and lifting of the core package and its anchor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;The side scan sonar operator advised me at the beginning of the day that he believed the esp package would be found on the bottom.&nbsp; He based this opinion on the data secured by his colleague almost two weeks ago.&nbsp; From his read of that run, he believed that the instrument was 15m off the bottom at that time.&nbsp; Depth at this site is 49m.&nbsp; He felt that the instrument was slowly sinking and that by today it was surly be on the sea floor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Todays side scan survey took approximately 90 minutes.&nbsp; They had acquired a strong signature on the core and calculated that it was at a depth of 65 feet (~20m). The package&nbsp; was still located within 10m of the original deployment site.&nbsp; They dropped a marker line with a float as close to the calculated position as possible.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;At this point divers equipped with twin 80 cu ft Nitrox cylinders and electric scooters dived on the marker.&nbsp; They had 70 minutes of search time.&nbsp; After 42 minutes an orange sausage float attached to a spectra lift line appeared.&nbsp; Then 10 minutes later a second lift bag attached to the EM cable appeared.&nbsp; The divers surfaced after a total bottom time of 62 minutes.&nbsp; Eight minutes to spare.&nbsp; We recovered the divers.&nbsp; They reported that the depth of top of the can was at 26 feet (~8m) right where it was supposed to be.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Recovery went smoothly using a single winch equipped with a capstan attachment.&nbsp; By alternately shifting the load from drum (used to lift anchor) and capstan (used to lift instrument we recovered the package and the anchor safely.{color}
{quote}
\\
\\  {color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford.

{color:#cc3300}July 6{color} \-\- Ship by truck D-ESP and supplies for JdF cruise.&nbsp; To Newport, OR.

{color:#cc3300}July 13{color} \-\- Sail for Axial and JdF (1 day late due to weather getting up to Newport)

{color:#cc0000}July 20{color} \-\- recall D-ESP.&nbsp; Recover all instruments.&nbsp; Two more days for Dave Clague.&nbsp; Ship returns July 23. \\

Aug 17 \-\- Matson picks up loaded ESP van.&nbsp; Genset on truck putting out >530V so our reefer unit will not start.&nbsp; Decide to send due to late hour and ship leaving tomorrow. ]]></property>
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<property name="body"><![CDATA[h1. Welcome to the G3 ESP and LRAUV Integration Page

\\

h3. Interface Control Documents

[^3G-LRAUV ICD ver1-0.doc]]]></property>
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<property name="body"><![CDATA[These are some notes about the servo model design and implementation.

Here are some of the plots generated from the unit tests:

!test_similar_to_servoTest.png!  
                    
!test_absMoves_with_direction_change_before_stop.png!

!test_setRawLimits_and_abrupt_stop_overCurrent.png!  

!test_getTimesForLimits.png!    
                     
!test_CompositeFunction_simple.png!                       

h1. Design in a nutshell

At time of writing the code resides in the 'servomodel' branch:
   https://github.com/MBARI-ESP/ESP2Gscript/tree/servomodel

The main source file, where the {{I2C::Servo::Model}} class is defined is: [servomodel.rb|https://github.com/MBARI-ESP/ESP2Gscript/blob/b63f5de300c96e1d2e1f68f7ac13eab01fa3e7f5/lib/i2c/model/servomodel.rb].

The servo simulation is modularized in a layered way. Elements of the modeling itself are under the {{ServoModeling}} module:

- {{Servo::Model}} and related elements are only concerned, in terms of the characterization of the velocity-position function, with {{ServoChannelSimulator}}.

- {{ServoChannelSimulator}} makes use of a {{FunctionFactory}} to keep and adjust the overall velocity-position function according to move commands.

- {{FunctionFactory}} facilitates the construction of {{Function}}'s.

- Possible {{Function}}'s are:
-- {{ConstantFunction}}: function always evaluating to {{\[0, pos\]}} for a given position
-- {{MonotoneFunction}}: captures the basic velocity profile of starting at velocity zero, and then going through acceleration, plateau, and deceleration zones. Starting at a given initial position, this function changes the position monotonically in a given direction.
-- {{CompositeFunction}}: function composed of the concatenation of multiple functions, each applied from a specific time wrt the previous one.


h1. Testing

All unit tests can be run at the command line as follows:

{code}
$ find lib/i2c/model -name \*_test.rb -exec ruby -I. -Ilib -Iutils {} \;
Loaded suite lib/i2c/model/servo/function_test
Started
..........
Finished in 0.015772 seconds.

10 tests, 607 assertions, 0 failures, 0 errors
Loaded suite lib/i2c/model/servo/functionfact_test
Started
..........
Finished in 0.030916 seconds.

10 tests, 1068 assertions, 0 failures, 0 errors
Loaded suite lib/i2c/model/servo/servochannelsim_test
Started
.......
Finished in 0.087462 seconds.

7 tests, 2531 assertions, 0 failures, 0 errors
Loaded suite lib/i2c/model/servomodel_test
Started
.......
Finished in 0.199393 seconds.

7 tests, 184 assertions, 0 failures, 0 errors
{code}
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
# [2014 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon ]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began

*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).
Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays
Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

MELO used was #300034012090780

location reported by MELO was-\- &nbsp; 33.4865 \-118.51285

*March 20*\--lost comms

*March 21*\--re-established comms and think problem in E/M cable.

*March 22*\--lost comms

*April 3*\--small boat to buoy to test E/M cable

*April 8*\--'rescue' mission


h4. {color:#ff00cc}ECOHAB--S. California{color}

April 1--Instruments deployed

&nbsp;MOE--inshore at&nbsp;

avg can depth \~9m

&nbsp;Bruce--offshore at

avg can depth \~19.5m ]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]]]></property>
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<property name="body"><![CDATA[h4. (as of Mar 28, 2013)


h3. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 day S. Cal ECOHAB w/ Bruce (Mar 2013)
* 15 day S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp; Bruce stopped working......

*25.5m (bare)*

*25.3m (bare)*
* Catalina Island replacement (April 2014).&nbsp; Installed April 8.

*21.5m (w/ floats)*
* Catalina Island (April 2014).&nbsp; used for 21 days.&nbsp; Failed after 4.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'popped' when we opened it.&nbsp; Photos [here|^Image 3.jpg|corrosion] and [here|^Image 2.jpg|salt crystals].

*15.6m (w/ floats)*
* 35 day S. Cal ECOHAB w/Mack (Mar 2013)
* 41 day MB ECOHAB w/Mack (Sep 2013)
* 30 day S. Cal ECOHAB w/Mack (Apr 2014)

*15.2m (w/ floats)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h3. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 17, 2008*

*11am-12*
Present: Jim, Doug, Addie, Scott, Cheri, Brent, Kevin


h3. Tech Transfer


h6. Discussion Items:

* Arm status update
* Environmental test chamber update

*Arm/Hand*.&nbsp; Removed Bruce from cold testing, and _almost_ finished with hand cold testing.&nbsp; Removed hand from Bruce and installed on Mack. Plan is to finish cold-test on hand and cold-test valves simultaneously on Mack.&nbsp; First priority in cold is to finish testing hand gripper.&nbsp; Once it passes, Mike will get green-light parts of the other hands (first 3 old action items).&nbsp; Order is placed with Maxxon for new forearm motors (maybe 6-8 weeks).&nbsp; Small order of fluidic fittings still needed for all of them.&nbsp; (Cheri)


*ETC* (Environmental Test Chamber).&nbsp; Cold box finished, electrical connectors in, fluidic connectors still need to be put in.&nbsp; New rotary valves all on Mack and being homed and calibrated.&nbsp; All we be ready for cold testing by end of day.

+Action Items+

ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp;

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}
{color:#000000}ACTION:{color}&nbsp; cannot purchase on 708 grant yet.&nbsp; 701312.04 should take all cost.&nbsp; Change:&nbsp; Order only 2 cans (Jim):&nbsp; {color:#0000ff}DONE; ordered 1-11-08{color}
ACTION:&nbsp; talk to Jose to figure a solution to broken home sensor cable. (Scott/Doug/Cheri){color:}&nbsp;{color} {color:#0000ff}DONE{color}
{color:}ACTION:&nbsp; Contact MAXON about forearm motors (Cheri){color} {color:#0000ff}DONE: ordered 1-14-08{color}
{color:#ff0000}ACTION{color}:&nbsp; confirm we have 3 swapable EM cables&nbsp; (Jim) {color:#0000ff}DONE: confer w/group and decide 1 spare is enough{color}


h3.


h3. MFB

Discussion Items:

•&nbsp;&nbsp;&nbsp; Syringe positioning

Syringe now oriented like other syringes on the core, i.e., pointing 'downward', and working well.&nbsp; Still waiting to test as several cables needed to be lengthened.

•&nbsp;&nbsp;&nbsp; Status of mixing column for extraction lysate.

Unable to build a 10cm mixing column because the use of 2 reducing unions requires a minimum of 50cm of tubing.&nbsp; Thus, mixing column is now 5x as long as it needs to be but waiting for Chris P. to do testing.&nbsp; Hope to test column next week around LLNL PCR visity.&nbsp;

ACTION:&nbsp; Jose to lengthen motor control cables (Addie).
ACTION:&nbsp; syringe motor mount.&nbsp; Mount 'upsidedown' for better lubrication.&nbsp; Changing motor for better gearing/speed ratio. (Addie)&nbsp; {color:#0000ff}DONE{color}
{color:#ff0000}ACTION{color}: confirm with email to Tony (Jim):&nbsp; {color:#0000ff}DONE{color}

h3. Software

Much discussion on how the code will be modified to accommodate a new thermal profile for puck heating.&nbsp; Brent suggested a very thorough plan of action, but was forced to accept a less elegant solution.&nbsp; Scott will provide nominal offsets and Brent will put in a mechanism to set gain/offset before every heating cycle.&nbsp; He has agreed to do this before the can cold-testing. (Brent)&nbsp;

Pressure tests; did four pressures.&nbsp; Chris P tried to grow lysate, but ran out of a reagent.&nbsp; We like 20-25psi---it's pumping like GG was. &nbsp; This number easy to change.&nbsp; He's made several parameters changeable.&nbsp; Chris P. knows most. &nbsp;&nbsp; Brent will create cheat-sheet for how these changes.

&nbsp;Firmware:&nbsp; servo-control works very well on MFB.&nbsp; Sampling at 64hz.&nbsp; this is different from all other dwarves so what should be do?&nbsp; Old code cannot change the divisor in the dwarves, but new Ruby can actually change the divisor, thus sampling at different rates.&nbsp; These are relatively large firmware modifications, so we will implement when the MFB goes in, NOT for Spring deployments.&nbsp;

Several small changes have resulted in a new firmware version that we +should+ update on Mack, Bruce, Neo.&nbsp; Brent will send email to everyone explaining changes.

+Action Items:+&nbsp;

ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent)
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)
ACTION:&nbsp; Update firmware on Mack, Bruce, Neo with the 'slightly modified version, and email the changes within this new firmware to everyone (Brent)

+Action Items from last week:+


ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code (Brent):&nbsp; {color:#ff0000}Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress{color}
{color:#ff0000}ACTION{color}:&nbsp; Test pressure stuff (above); if problems, then heating stuff is dropped.&nbsp; {color:#0000ff}DONE (we believe 20-25psi delta will work like GG){color}
{color:#000000}ACTION{color}:&nbsp; Chris to give Brent water sample for running next week.&nbsp; Test running on bench at various pressures and run lysate test to test effects of different pressures (Chris/Brent) {color:#0000ff}DONE{color}



h3. Sphere and 4K DWSMS

Oil for DWSM has arrived and currenly being cold-tested.&nbsp; Doug met with local micro-pump rep, and is getting close to choosing the pumps he wants.&nbsp; All parts are ordered for the plastic model, which he will build in the Bldg B lab.&nbsp; He has the layout design and partial design for vavle actuators.&nbsp;

Nilo has inventoried all pucks and is receiving instruction on how to get them laser-etched.&nbsp; Will take first batch for etching next week.&nbsp; Following this [numbering scheme|ESPAPP:Puck Numbering System]. \\

{color:#ff0000}ACTION{color}:&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
ACTION: Get quote for surface cans from Gene and place order (Jim):&nbsp; {color:#0000ff}DONE{color}
{color:#000000}ACTION{color}: discuss procurement and build schedule for next 2 cores (WHOI and CMORE funded) at 1-24-2008 mtg (in two weeks) {color:#ff0000}next meeting{color}.&nbsp;
h3. GUI Development

Kevin trying to have the Mission Script GUI in our hands before the [2008 Q1-Q2 Schedule].
\\ \\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 17, 2008*

*11am-12*
Present: Jim, Doug, Addie, Scott, Cheri


h4. Tech Transfer

Action Items from last week:

ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}
ACTION: check with Jose and Tom about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose still diggin through BOM to figure out what we can order&nbsp; (1/4 way through)&nbsp; has mad the first pass through and looks like they are still available.&nbsp; Jose getting price and lead time on everything.


{color:#000000}ACTION:{color}&nbsp; cannot purchase on 708 grant yet.&nbsp; 701312.04 should take all cost.&nbsp; Change:&nbsp; Order only 2 cans (Jim):&nbsp; {color:#0000ff}DONE; ordered 1-11-08{color}
ACTION:&nbsp; talk to Jose to figure a solution to broken home sensor cable. (Scott/Doug/Cheri){color:}&nbsp;{color} {color:#0000ff}DONE{color}
{color:}ACTION:&nbsp; Contact MAXON about forearm motors (Cheri){color} {color:#0000ff}DONE: ordered 1-14-08{color}
{color:#ff0000}ACTION{color}:&nbsp; confirm we have 3 swapable EM cables and purchase spares from 701312.04 (including labor) (Jim?)

h3. Discussion Items:

* Arm status update
* Environmental test chamber update

Cold box finished, electrical connectors in, Fluidic connectors still need to be put in.&nbsp; New rotary valves all on Mack and being homed and calibrated.&nbsp; All we be ready for cold testing by end of day.&nbsp;

Hand.&nbsp; Took Bruce's out and it works great in MACK. Plan is to cold-test both hand and valves simultaneously on Mack.&nbsp; First priority in cold is to finish testing on hand gripper.&nbsp; Once it passes, Mike will get green-light parts of the other hands.&nbsp; Order is placed with Maxxon for new forearm motors (maybe 6-8 weeks).&nbsp; Small order of fluidic fittings still needed for all of them.&nbsp; (Cheri)&nbsp;

h3. MFB

ACTION:&nbsp; syringe motor mount.&nbsp; Mount 'upsidedown' for better lubrication.&nbsp; Changing motor for better gearing/speed ratio. (Addie)&nbsp; {color:#ff0000}SEE BELOW{color}
{color:#ff0000}ACTION{color}: confirm with email to Tony (Jim):&nbsp; {color:#0000ff}DONE{color}

Discussion Items:

•&nbsp;&nbsp;&nbsp; Syringe positioning

Syringe now like core-syringes and working well.&nbsp; Still waiting on motor-cable--Jose should be done by today (Addie).&nbsp;

•&nbsp;&nbsp;&nbsp; Status of mixing column for extraction lysate.

Built with 2 reducing unions and have 10cm of tubing, but union need it to be 50cm.&nbsp; So mixing column is now 5x as long as it needs to be but waiting for Chris P. to do testing.&nbsp; testing with next week hopefully.&nbsp;

h3. Software

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code (Brent):&nbsp; {color:#ff0000}Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress:{color} Wayne still on vacation
{color:#ff0000}ACTION{color}:&nbsp; Chris to give Brent water sample for running next week.&nbsp; Test running on bench at various pressures and run lysate test to test effects of different pressures (Chris/Brent) {color:#0000ff}DONE{color}
{color:#ff0000}ACTION{color}:&nbsp; Will change the hardware, and look at offsets (Scott)
{color:#ff0000}ACTION{color}:&nbsp; Test pressure stuff (above); if problems, then heating stuff is dropped

Temp calibration.&nbsp; Brent needs to put hooks into the code so that we can empirically figure the offsets and insert them.&nbsp; He has agreed to do this before the can cold-testing. (Brent)&nbsp;

Scott will provide nominal offsets and Brent going to put mechansism to set gain/offset before every heating cycle.

Pressure tests; did four pressures.&nbsp; Chris P tried to grow lysate, but ran out of a reagent.&nbsp; We like 20-25psi---it's pumping like GG was. &nbsp; This number easy to change.&nbsp; He's made several parameters changeable.&nbsp; Chris P. knows most. &nbsp;&nbsp; Brent will create cheat-sheet for how these changes.

&nbsp;Firmware:&nbsp; servo-control works very well on MFB.&nbsp; Sampling at 64hz.&nbsp; this is different from all other dwarves so what should be do.&nbsp; Old code cannot change the divisor in the dwarves, but new Ruby can actually change the divisor, thus sampling at different rates.&nbsp; These firmware modifications should go in when the MFB goes in.&nbsp;

Several small changes have resulted in a new firmware version that we should update on Mack, Bruce, Neo.&nbsp; Brent will send email to everyone explaining changes.&nbsp;\\

h3. Sphere and 4K DWSMS

ACTION:&nbsp; Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott).&nbsp; {color:#ff0000}In progress{color}.&nbsp; Maybe take early next week


msut spec hole and fix the original drawings.&nbsp; Also should talk to manufacturers.&nbsp;\\

ACTION: will try and have model done by end of Jan--depends on pumps (Doug) {color:#ff0000}In progress{color}

meet with Ryan Herkow.&nbsp; Local rep for micro-pump.&nbsp; He has gotten close to choosing the pump her wants.&nbsp; All parts ordered for model.&nbsp; using 2L Steeden bags.&nbsp; He has the layout design and a partial design for valve actuators.&nbsp;


ACTION: Get quote for surface cans from Gene and place order (Jim):&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price

Oil is in and being cold tested.

has layout and partial design for valve actuators&nbsp;

Discussion Items:

•&nbsp;&nbsp;&nbsp; Status of new puck order
One set (carousel) by March 3; we need to tell them when we need the next set.

•&nbsp;&nbsp;&nbsp; Order and manufacture of screens, frits, polysulfone
photofab gave too large holes so too weak.&nbsp; Laser cut would be more accurate.&nbsp; Give them (photofab) hard spec with feedback.&nbsp; Chris has info on the scintered frits and ordering specs.

{color:#ff0000}ACTION{color}:&nbsp; get inventory from Roman (Jim/Roman): laser-etch pore size for scintered frits

•&nbsp;&nbsp;&nbsp; Procurement schedule for next 2 cores

We don't have money from WHOI until late 2008.&nbsp; CMORE we're in the middle of that year

{color:#ff0000}ACTION{color}: discuss build schedule for next 2 cores at 1-24-2008 mtg (in two weeks).&nbsp;

h3. GUI Development

&nbsp;*Progress update*
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 17, 2008*

*11am-12*
Present:&nbsp;

h4. Tech Transfer

Action Items from last week:

ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}
ACTION: check with Jose and Tom about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose still diggin through BOM to figure out what we can order&nbsp; (1/4 way through)
{color:#000000}ACTION:{color}&nbsp; cannot purchase on 708 grant yet.&nbsp; 701312.04 should take all cost.&nbsp; Change:&nbsp; Order only 2 cans (Jim):&nbsp; {color:#0000ff}DONE; ordered 1-11-08{color}
ACTION:&nbsp; talk to Jose to figure a solution to broken home sensor cable. (Scott/Doug/Cheri){color:}&nbsp;{color} {color:#0000ff}DONE{color}
{color:}ACTION:&nbsp; Contact MAXON about forearm motors (Cheri){color} {color:#0000ff}DONE: ordered 1-14-08{color}
{color:#ff0000}ACTION{color}:&nbsp; confirm we have 3 swapable EM cables and purchase spares from 701312.04 (including labor) (Jim?)

h3. Discussion Items:

* Arm status update
* Environmental test chamber update

h3. MFB

ACTION:&nbsp; syringe motor mount.&nbsp; Mount 'upsidedown' for better lubrication.&nbsp; Changing motor for better gearing/speed ratio. (Addie)&nbsp; {color:#ff0000}SEE BELOW{color}
{color:#ff0000}ACTION{color}: confirm with email to Tony (Jim):&nbsp; {color:#0000ff}DONE{color}

Discussion Items:

•&nbsp;&nbsp;&nbsp; Syringe positioning

•&nbsp;&nbsp;&nbsp; Status of mixing column for extraction lysate.


h3. Software

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code (Brent):&nbsp; {color:#ff0000}Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress:{color} Wayne still on vacation
{color:#ff0000}ACTION{color}:&nbsp; Chris to give Brent water sample for running next week.&nbsp; Test running on bench at various pressures and run lysate test to test effects of different pressures (Chris/Brent) {color:#0000ff}DONE{color}
{color:#ff0000}ACTION{color}:&nbsp; Will change the hardware, and look at offsets (Scott)
{color:#ff0000}ACTION{color}:&nbsp; Test pressure stuff (above); if problems, then heating stuff is dropped&nbsp;

h3. Sphere and 4K DWSMS

ACTION:&nbsp; Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott).&nbsp; {color:#ff0000}In progress{color}.

ACTION: will try and have model done by end of Jan--depends on pumps (Doug) {color:#ff0000}In progress{color}

ACTION: Get quote for surface cans from Gene and place order (Jim):&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price

Discussion Items:

•&nbsp;&nbsp;&nbsp; Status of new puck order
One set (carousel) by March 3; we need to tell them when we need the next set.

•&nbsp;&nbsp;&nbsp; Order and manufacture of screens, frits, polysulfone
photofab gave too large holes so too weak.&nbsp; Laser cut would be more accurate.&nbsp; Give them (photofab) hard spec with feedback.&nbsp; Chris has info on the scintered frits and ordering specs.

{color:#ff0000}ACTION{color}:&nbsp; get inventory from Roman (Jim/Roman): laser-etch pore size for scintered frits

•&nbsp;&nbsp;&nbsp; Procurement schedule for next 2 cores

We don't have money from WHOI until late 2008.&nbsp; CMORE we're in the middle of that year

{color:#ff0000}ACTION{color}: discuss build schedule for next 2 cores at 1-24-2008 mtg (in two weeks).&nbsp;

h3. GUI Development

&nbsp;*Progress update*
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics worksheet 17JulFeb08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2019Feb08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science
# [2008 Deployments]]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2017JulFeb08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[# [Comments from July 9, 2008 Design Review]
# [Doug's collected comments July 9 Design Review]]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 17, 2008*

*11am-12*
Present:&nbsp;

h4. Tech Transfer

Action Items from last week:

ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}
ACTION: check with Jose and Tom about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose still diggin through BOM to figure out what we can order&nbsp; (1/4 way through)
{color:#000000}ACTION:{color}&nbsp; cannot purchase on 708 grant yet.&nbsp; 701312.04 should take all cost.&nbsp; Change:&nbsp; Order only 2 cans (Jim):&nbsp; {color:#0000ff}DONE; ordered 1-11-08{color}
ACTION:&nbsp; talk to Jose to figure a solution to broken home sensor cable. (Scott/Doug/Cheri){color:}&nbsp;{color} {color:#0000ff}DONE{color}
{color:}ACTION:&nbsp; Contact MAXON about forearm motors (Cheri){color} {color:#0000ff}DONE: ordered 1-14-08{color}

h3.

{color:#ff0000}ACTION{color}:&nbsp; confirm we have 3 swapable EM cables and purchase spares from 701312.04 (including labor) (Jim?)

h3.

Discussion Items:

* Arm status update
* Environmental test chamber update\\

h3. MFB

ACTION:&nbsp; syringe motor mount.&nbsp; Mount 'upsidedown' for better lubrication.&nbsp; Changing motor for better gearing/speed ratio. (Addie)&nbsp; {color:#ff0000}SEE BELOW{color}
{color:#ff0000}ACTION{color}: confirm with email to Tony (Jim):&nbsp; {color:#0000ff}DONE{color}

Discussion Items:

\\

•&nbsp;&nbsp;&nbsp; Syringe lubrication

Syringe motor has been changed to one with higher encoder count.&nbsp; Should be no problem to get slower speed; pin numbers were different (10 new vs 6 old).&nbsp; Brent and Addie working on calibrating it.&nbsp; Config file is now cleaned and only contains MFB stuff.&nbsp; Flipping syringe will allow lube to sit on top of plunger.&nbsp; Syringe will be flipped.

•&nbsp;&nbsp;&nbsp; Mixing column for extraction lysate.&nbsp; Discuss construction.

Cannot put PEEK 2ml ID tubing into our smaller fittings.&nbsp; But can use 1/4-28 fitting normally.&nbsp; So Addie instructed to build simply stand-pipe structure with PEEK.&nbsp; May look at Optimize.com who make HPLC mixing chambers to see if they have these chambers. Addie going to check out standpipe design/structure.

h3. Software

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code (Brent):&nbsp; {color:#ff0000}Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress:{color} Wayne still on vacation
{color:#ff0000}ACTION{color}:&nbsp; Chris to give Brent water sample for running next week.&nbsp; Test running on bench at various pressures and run lysate test to test effects of different pressures (Chris/Brent) {color:#0000ff}DONE{color}

Discussion Items:
•&nbsp;&nbsp;&nbsp; Themal control hardware.&nbsp; Necessitate a firmware change?

Scott has a new sensor setup.&nbsp; Goal would be to eliminate funny ramps in RUBY to avoid overshooting.&nbsp; These controls are already in the DC motor controllers, so should we use this control in the temp control?&nbsp; Worry is it's a big change.&nbsp; Firmware/Ruby must both change.&nbsp; This started because we don't always 'get' to our required temperature; its a function of ambient in the can.&nbsp; Chris; if offset is pretty well known, then we could live with it, if offset is big, it could screw up our array results.&nbsp; We can change the hardware, but getting software changed over may take too long.

{color:#ff0000}ACTION{color}:&nbsp; Will change the hardware, and look at offsets (Scott)

This will dictate next step.&nbsp;

•&nbsp;&nbsp;&nbsp; Modification of friction compensation w/in servo code.

In progress, but not as important as heating offsets.

•&nbsp;&nbsp;&nbsp; Other software changes and test plan for their implementation

{color:#ff0000}ACTION{color}:&nbsp; Test pressure stuff (above); if problems, then heating stuff is dropped&nbsp;

h3. Sphere and 4K DWSMS

ACTION:&nbsp; Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott).&nbsp; {color:#ff0000}In progress{color}.

ACTION: will try and have model done by end of Jan--depends on pumps (Doug) {color:#ff0000}In progress{color}

ACTION: Get quote for surface cans from Gene and place order (Jim):&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price

Discussion Items:

•&nbsp;&nbsp;&nbsp; Serial numbering of old pucks
put this on Confluence

•&nbsp;&nbsp;&nbsp; Status of new puck order
One set (carousel) by March 3; we need to tell them when we need the next set.

•&nbsp;&nbsp;&nbsp; Order and manufacture of screens, frits, polysulfone
photofab gave too large holes so too weak.&nbsp; Laser cut would be more accurate.&nbsp; Give them (photofab) hard spec with feedback.&nbsp; Chris has info on the scintered frits and ordering specs.

{color:#ff0000}ACTION{color}:&nbsp; get inventory from Roman (Jim/Roman): laser-etch pore size for scintered frits

•&nbsp;&nbsp;&nbsp; Pressure pots ordered? Yes
•&nbsp;&nbsp;&nbsp; Status of 4K sphere:&nbsp; 2-piece pattern pictures sent to us: shipping them over to casting house

•&nbsp;&nbsp;&nbsp; Procurement schedule for next 2 cores

We don't have money from WHOI until late 2008.&nbsp; CMORE we're in the middle of that year

{color:#ff0000}ACTION{color}: discuss build schedule for next 2 cores at 1-24-2008 mtg (in two weeks).&nbsp;

h3. GUI Development

&nbsp;Kevin updated on GUI development.&nbsp; He would like to use his GUI tool to generate a mission-script for the Feb cold-room test.&nbsp; He needs reagent volumes to get accurate usage display.&nbsp; We will want to generate mission script the last week in January.&nbsp; Will meet tomorrow (Jan 11) to discuss volumes with him.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 17, 2008*

*11am-12*
Present:&nbsp;

h4. Tech Transfer

Action Items from last week:

ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}
ACTION: check with Jose and Tom about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose still diggin through BOM to figure out what we can order&nbsp; (1/4 way through)
{color:#000000}ACTION:{color}&nbsp; cannot purchase on 708 grant yet.&nbsp; 701312.04 should take all cost.&nbsp; Change:&nbsp; Order only 2 cans (Jim):&nbsp; {color:#0000ff}DONE; ordered 1-11-08{color}
ACTION:&nbsp; talk to Jose to figure a solution to broken home sensor cable. (Scott/Doug/Cheri){color:}&nbsp;{color} {color:#0000ff}DONE{color}
{color:}ACTION:&nbsp; Contact MAXON about forearm motors (Cheri){color} {color:#0000ff}DONE: ordered 1-14-08{color}

h3.

{color:#ff0000}ACTION{color}:&nbsp; confirm we have 3 swapable EM cables and purchase spares from 701312.04 (including labor) (Jim?)

h3.

Discussion Items:
•&nbsp;&nbsp;&nbsp; Mooring supplies for network deployment

No one knows everything.&nbsp; We can get by with 2, but we really need 3.&nbsp; Doug says it's 6 months of Jim S. time, but Chris thought 1 month.&nbsp; Discussion ensued on what was necessary and we agreed that we could get by with our two complete moorings with appropriate spare parts.

•&nbsp;&nbsp;&nbsp; Update on test chamber and test chamber fixtures

•&nbsp;&nbsp;&nbsp; Arm status (see above)

h3. MFB

ACTION:&nbsp; syringe motor mount.&nbsp; Mount 'upsidedown' for better lubrication.&nbsp; Changing motor for better gearing/speed ratio. (Addie)&nbsp; {color:#ff0000}SEE BELOW{color}
{color:#ff0000}ACTION{color}: confirm with email to Tony (Jim):&nbsp; {color:#0000ff}DONE{color}

Discussion Items:

\\

•&nbsp;&nbsp;&nbsp; Syringe lubrication

Syringe motor has been changed to one with higher encoder count.&nbsp; Should be no problem to get slower speed; pin numbers were different (10 new vs 6 old).&nbsp; Brent and Addie working on calibrating it.&nbsp; Config file is now cleaned and only contains MFB stuff.&nbsp; Flipping syringe will allow lube to sit on top of plunger.&nbsp; Syringe will be flipped.

•&nbsp;&nbsp;&nbsp; Mixing column for extraction lysate.&nbsp; Discuss construction.

Cannot put PEEK 2ml ID tubing into our smaller fittings.&nbsp; But can use 1/4-28 fitting normally.&nbsp; So Addie instructed to build simply stand-pipe structure with PEEK.&nbsp; May look at Optimize.com who make HPLC mixing chambers to see if they have these chambers. Addie going to check out standpipe design/structure.

h3. Software

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code (Brent):&nbsp; {color:#ff0000}Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress:{color} Wayne still on vacation
{color:#ff0000}ACTION{color}:&nbsp; Chris to give Brent water sample for running next week.&nbsp; Test running on bench at various pressures and run lysate test to test effects of different pressures (Chris/Brent) {color:#0000ff}DONE{color}

Discussion Items:
•&nbsp;&nbsp;&nbsp; Themal control hardware.&nbsp; Necessitate a firmware change?

Scott has a new sensor setup.&nbsp; Goal would be to eliminate funny ramps in RUBY to avoid overshooting.&nbsp; These controls are already in the DC motor controllers, so should we use this control in the temp control?&nbsp; Worry is it's a big change.&nbsp; Firmware/Ruby must both change.&nbsp; This started because we don't always 'get' to our required temperature; its a function of ambient in the can.&nbsp; Chris; if offset is pretty well known, then we could live with it, if offset is big, it could screw up our array results.&nbsp; We can change the hardware, but getting software changed over may take too long.

{color:#ff0000}ACTION{color}:&nbsp; Will change the hardware, and look at offsets (Scott)

This will dictate next step.&nbsp;

•&nbsp;&nbsp;&nbsp; Modification of friction compensation w/in servo code.

In progress, but not as important as heating offsets.

•&nbsp;&nbsp;&nbsp; Other software changes and test plan for their implementation

{color:#ff0000}ACTION{color}:&nbsp; Test pressure stuff (above); if problems, then heating stuff is dropped&nbsp;

h3. Sphere and 4K DWSMS

ACTION:&nbsp; Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott).&nbsp; {color:#ff0000}In progress{color}.

ACTION: will try and have model done by end of Jan--depends on pumps (Doug) {color:#ff0000}In progress{color}

ACTION: Get quote for surface cans from Gene and place order (Jim):&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price

Discussion Items:

•&nbsp;&nbsp;&nbsp; Serial numbering of old pucks
put this on Confluence

•&nbsp;&nbsp;&nbsp; Status of new puck order
One set (carousel) by March 3; we need to tell them when we need the next set.

•&nbsp;&nbsp;&nbsp; Order and manufacture of screens, frits, polysulfone
photofab gave too large holes so too weak.&nbsp; Laser cut would be more accurate.&nbsp; Give them (photofab) hard spec with feedback.&nbsp; Chris has info on the scintered frits and ordering specs.

{color:#ff0000}ACTION{color}:&nbsp; get inventory from Roman (Jim/Roman): laser-etch pore size for scintered frits

•&nbsp;&nbsp;&nbsp; Pressure pots ordered? Yes
•&nbsp;&nbsp;&nbsp; Status of 4K sphere:&nbsp; 2-piece pattern pictures sent to us: shipping them over to casting house

•&nbsp;&nbsp;&nbsp; Procurement schedule for next 2 cores

We don't have money from WHOI until late 2008.&nbsp; CMORE we're in the middle of that year

{color:#ff0000}ACTION{color}: discuss build schedule for next 2 cores at 1-24-2008 mtg (in two weeks).&nbsp;

h3. GUI Development

&nbsp;Kevin updated on GUI development.&nbsp; He would like to use his GUI tool to generate a mission-script for the Feb cold-room test.&nbsp; He needs reagent volumes to get accurate usage display.&nbsp; We will want to generate mission script the last week in January.&nbsp; Will meet tomorrow (Jan 11) to discuss volumes with him.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 10, 2008*

*10:30am-12*
Present:&nbsp; Jim, Chris S., Brent, Doug, Kevin G, Cheri, Addie, Scott

h4. *After today meetings will be 11-12am*&nbsp;


h3. Tech Transfer

Action Items from last week:

ACTION: Brent will show Cheri and Addie how to read log (Brent & Cheri & Addie)&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; run a sample on GG to compare pressures to NEO (Scott)&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}
ACTION: check with Jose and Tom about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose still diggin through BOM to figure out what we can order&nbsp; (1/4 way through)
ACTION: discuss test box design with Jim Scholfield (Cheri)&nbsp; {color:#0000ff}DONE:{color} Jim and Cheri and Scott discussed design; he's ordering parts.&nbsp; Maybe end of next.
ACTION:&nbsp; move connectors from 1K to the test box (Doug & Cheri)&nbsp; {color:#0000ff}DONE{color}: Been pulled off 1K and now at Jim S (electrical).&nbsp; Fluidic connectors--we are going to use ones that Mike made.&nbsp; Doug thinks they are in lab downstairs.
ACTION: Clean B125 lab for CMORE visit (everyone)

Discussion Items:
•&nbsp;&nbsp;&nbsp; Surface can quote from IMT:&nbsp; 3 cans = \~$37K

{color:#ff0000}ACTION{color}:&nbsp; cannot purchase on 708 grant yet.&nbsp; 701312.04 should take all cost.&nbsp; Change:&nbsp; Order only 2 cans (Jim)

•&nbsp;&nbsp;&nbsp; Mooring supplies for network deployment

No one knows everything.&nbsp; We can get by with 2, but we really need 3.&nbsp; Doug says it's 6 months of Jim S. time, but Chris thought 1 month.&nbsp; Discussion ensued on what was necessary and we agreed that we could get by with our two complete moorings with appropriate spare parts.

{color:#ff0000}ACTION{color}:&nbsp; confirm we have 3 swapable EM cables and purchase spares from 701312.04 (including labor) (Jim?)

•&nbsp;&nbsp;&nbsp; Update on test chamber and test chamber fixtures

•&nbsp;&nbsp;&nbsp; Arm status (see above)

Failure last week was due to an assembly issue on arm that caused binding.&nbsp; Reassembly found broken wires in home sensor.&nbsp; Friday was working great at 10 degrees all weekend.&nbsp; Checked Monday morning it looked fine.&nbsp; Lowered temp to 2C and Tuesday found ribbon cable home sensor cable was broken.&nbsp; There is a loop for a strain relief.&nbsp; Brent suggests mylar cable used in printer.&nbsp; Chris suggests a 'ticker' to count cycles so we know when things should be changed.&nbsp; Revalving has started on Mack; 7 of 8 have been done.&nbsp; Modifying mount on 8th one.&nbsp; Should be done by Monday.

We will use 'non-ideal' arms for Spring deployment, but when we order new hands, we will order the correct 4-bar holes.&nbsp;

{color:#ff0000}ACTION{color}:&nbsp; talk to Jose to figure a solution to broken home sensor cable. (Scott/Doug/Cheri)

{color:#ff0000}ACTION{color}: Contact MAXON about forearm motors (Cheri)&nbsp;

h3. MFB

ACTION:&nbsp; Order custom valve heads (Addie)&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; syringe motor mount.&nbsp; Mount 'upsidedown' for better lubrication.&nbsp; Changing motor for better gearing/speed ratio. (Addie)&nbsp; {color:#ff0000}SEE BELOW{color}
ACTION:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (Scott/Brent/Addie):&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; Sleepy board given to Brent, w/ Addie using a dwarf board (Addie):&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; talk to Tony and get timeline on next MFB (Jim):&nbsp; {color:#0000ff}DONE{color}

Discussion Items:
•&nbsp;&nbsp;&nbsp; LLNL schedule---Tony coming Jan. 23.&nbsp; DONE

{color:#ff0000}ACTION{color}: confirm with email to Tony (Jim)

•&nbsp;&nbsp;&nbsp; Syringe lubrication

Syringe motor has been changed to one with higher encoder count.&nbsp; Should be no problem to get slower speed; pin numbers were different (10 new vs 6 old).&nbsp; Brent and Addie working on calibrating it.&nbsp; Config file is now cleaned and only contains MFB stuff.&nbsp; Flipping syringe will allow lube to sit on top of plunger.&nbsp; Syringe will be flipped.

•&nbsp;&nbsp;&nbsp; Mixing column for extraction lysate.&nbsp; Discuss construction.

Cannot put PEEK 2ml ID tubing into our smaller fittings.&nbsp; But can use 1/4-28 fitting normally.&nbsp; So Addie instructed to build simply stand-pipe structure with PEEK.&nbsp; May look at Optimize.com who make HPLC mixing chambers to see if they have these chambers. Addie going to check out standpipe design/structure.

h3. Software

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; change laptops and ARM boards and install the new Ruby interpreter (Brent):&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code (Brent):&nbsp; {color:#ff0000}Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress:{color} Wayne still on vacation

Discussion Items:
•&nbsp;&nbsp;&nbsp; Sampling technique.&nbsp; Greater pressure or 'pulsing' or both?

Brent has maxed the vacuum in the syringe without cavitation but unknown if this is how 'natural' water works.&nbsp; Chris can provide natural sample.&nbsp; To get more sample volume do we want to experiment with a greater deltaP?&nbsp;

{color:#ff0000}ACTION{color}:&nbsp; Chris to give Brent water sample for running next week.&nbsp; Test running on bench at various pressures and run lysate test to test effects of different pressures (Chris/Brent)&nbsp;

•&nbsp;&nbsp;&nbsp; Themal control hardware.&nbsp; Necessitate a firmware change?

Scott has a new sensor setup.&nbsp; Goal would be to eliminate funny ramps in RUBY to avoid overshooting.&nbsp; These controls are already in the DC motor controllers, so should we use this control in the temp control?&nbsp; Worry is it's a big change.&nbsp; Firmware/Ruby must both change.&nbsp; This started because we don't always 'get' to our required temperature; its a function of ambient in the can.&nbsp; Chris; if offset is pretty well known, then we could live with it, if offset is big, it could screw up our array results.&nbsp; We can change the hardware, but getting software changed over may take too long.

{color:#ff0000}ACTION{color}:&nbsp; Will change the hardware, and look at offsets (Scott)

This will dictate next step.&nbsp;

•&nbsp;&nbsp;&nbsp; Modification of friction compensation w/in servo code.

In progress, but not as important as heating offsets.

•&nbsp;&nbsp;&nbsp; Other software changes and test plan for their implementation

{color:#ff0000}ACTION{color}:&nbsp; Test pressure stuff (above); if problems, then heating stuff is dropped&nbsp;

h3. Sphere and 4K DWSMS

ACTION:&nbsp; Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott).&nbsp; {color:#ff0000}In progress{color}.

Get Nilo to take lead on this with Roman oversight.

ACTION: will try and have model done by end of Jan--depends on pumps (Doug) {color:#ff0000}In progress{color}

Can readily put together plastic housing.&nbsp; Still working on type of pumps

ACTION: Get quote for surface cans from Gene and place order (Jim):&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price

Discussion Items:

•&nbsp;&nbsp;&nbsp; Serial numbering of old pucks
put this on Confluence

•&nbsp;&nbsp;&nbsp; Status of new puck order
One set (carousel) by March 3; we need to tell them when we need the next set.

•&nbsp;&nbsp;&nbsp; Order and manufacture of screens, frits, polysulfone
photofab gave too large holes so too weak.&nbsp; Laser cut would be more accurate.&nbsp; Give them (photofab) hard spec with feedback.&nbsp; Chris has info on the scintered frits and ordering specs.

{color:#ff0000}ACTION{color}:&nbsp; get inventory from Roman (Jim/Roman): laser-etch pore size for scintered frits

•&nbsp;&nbsp;&nbsp; Pressure pots ordered? Yes
•&nbsp;&nbsp;&nbsp; Status of 4K sphere:&nbsp; 2-piece pattern pictures sent to us: shipping them over to casting house

•&nbsp;&nbsp;&nbsp; Procurement schedule for next 2 cores

We don't have money from WHOI until late 2008.&nbsp; CMORE we're in the middle of that year

{color:#ff0000}ACTION{color}: discuss build schedule for next 2 cores at 1-24-2008 mtg (in two weeks).&nbsp;

h3. GUI Development

&nbsp;Kevin updated on GUI development.&nbsp; He would like to use his GUI tool to generate a mission-script for the Feb cold-room test.&nbsp; He needs reagent volumes to get accurate usage display.&nbsp; We will want to generate mission script the last week in January.&nbsp; Will meet tomorrow (Jan 11) to discuss volumes with him.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 17, 2008*

*11am-12*
Present:&nbsp;

h4. Tech Transfer

Action Items from last week:

ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}
ACTION: check with Jose and Tom about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose still diggin through BOM to figure out what we can order&nbsp; (1/4 way through)
{color:#000000}ACTION:{color}&nbsp; cannot purchase on 708 grant yet.&nbsp; 701312.04 should take all cost.&nbsp; Change:&nbsp; Order only 2 cans (Jim):&nbsp; {color:#0000ff}DONE; ordered 1-11-08{color}
ACTION:&nbsp; talk to Jose to figure a solution to broken home sensor cable. (Scott/Doug/Cheri){color:}&nbsp;{color} {color:#0000ff}DONE{color}
{color:}ACTION:&nbsp; Contact MAXON about forearm motors (Cheri){color} {color:#0000ff}DONE: ordered 1-14-08{color}

h3.

{color:#ff0000}ACTION{color}:&nbsp; confirm we have 3 swapable EM cables and purchase spares from 701312.04 (including labor) (Jim?)

h3.

Discussion Items:
•&nbsp;&nbsp;&nbsp; Mooring supplies for network deployment

No one knows everything.&nbsp; We can get by with 2, but we really need 3.&nbsp; Doug says it's 6 months of Jim S. time, but Chris thought 1 month.&nbsp; Discussion ensued on what was necessary and we agreed that we could get by with our two complete moorings with appropriate spare parts.

•&nbsp;&nbsp;&nbsp; Update on test chamber and test chamber fixtures

•&nbsp;&nbsp;&nbsp; Arm status (see above)

h3. MFB

ACTION:&nbsp; syringe motor mount.&nbsp; Mount 'upsidedown' for better lubrication.&nbsp; Changing motor for better gearing/speed ratio. (Addie)&nbsp; {color:#ff0000}SEE BELOW{color}
{color:#ff0000}ACTION{color}: confirm with email to Tony (Jim):&nbsp; {color:#0000ff}DONE{color}


Discussion Items:

\\

•&nbsp;&nbsp;&nbsp; Syringe lubrication

Syringe motor has been changed to one with higher encoder count.&nbsp; Should be no problem to get slower speed; pin numbers were different (10 new vs 6 old).&nbsp; Brent and Addie working on calibrating it.&nbsp; Config file is now cleaned and only contains MFB stuff.&nbsp; Flipping syringe will allow lube to sit on top of plunger.&nbsp; Syringe will be flipped.

•&nbsp;&nbsp;&nbsp; Mixing column for extraction lysate.&nbsp; Discuss construction.

Cannot put PEEK 2ml ID tubing into our smaller fittings.&nbsp; But can use 1/4-28 fitting normally.&nbsp; So Addie instructed to build simply stand-pipe structure with PEEK.&nbsp; May look at Optimize.com who make HPLC mixing chambers to see if they have these chambers. Addie going to check out standpipe design/structure.

h3. Software

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; change laptops and ARM boards and install the new Ruby interpreter (Brent):&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code (Brent):&nbsp; {color:#ff0000}Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress:{color} Wayne still on vacation

Discussion Items:
•&nbsp;&nbsp;&nbsp; Sampling technique.&nbsp; Greater pressure or 'pulsing' or both?

Brent has maxed the vacuum in the syringe without cavitation but unknown if this is how 'natural' water works.&nbsp; Chris can provide natural sample.&nbsp; To get more sample volume do we want to experiment with a greater deltaP?&nbsp;

{color:#ff0000}ACTION{color}:&nbsp; Chris to give Brent water sample for running next week.&nbsp; Test running on bench at various pressures and run lysate test to test effects of different pressures (Chris/Brent)&nbsp;

•&nbsp;&nbsp;&nbsp; Themal control hardware.&nbsp; Necessitate a firmware change?

Scott has a new sensor setup.&nbsp; Goal would be to eliminate funny ramps in RUBY to avoid overshooting.&nbsp; These controls are already in the DC motor controllers, so should we use this control in the temp control?&nbsp; Worry is it's a big change.&nbsp; Firmware/Ruby must both change.&nbsp; This started because we don't always 'get' to our required temperature; its a function of ambient in the can.&nbsp; Chris; if offset is pretty well known, then we could live with it, if offset is big, it could screw up our array results.&nbsp; We can change the hardware, but getting software changed over may take too long.

{color:#ff0000}ACTION{color}:&nbsp; Will change the hardware, and look at offsets (Scott)

This will dictate next step.&nbsp;

•&nbsp;&nbsp;&nbsp; Modification of friction compensation w/in servo code.

In progress, but not as important as heating offsets.

•&nbsp;&nbsp;&nbsp; Other software changes and test plan for their implementation

{color:#ff0000}ACTION{color}:&nbsp; Test pressure stuff (above); if problems, then heating stuff is dropped&nbsp;

h3. Sphere and 4K DWSMS

ACTION:&nbsp; Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott).&nbsp; {color:#ff0000}In progress{color}.

Get Nilo to take lead on this with Roman oversight.

ACTION: will try and have model done by end of Jan--depends on pumps (Doug) {color:#ff0000}In progress{color}

Can readily put together plastic housing.&nbsp; Still working on type of pumps

ACTION: Get quote for surface cans from Gene and place order (Jim):&nbsp; {color:#0000ff}DONE{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price

Discussion Items:

•&nbsp;&nbsp;&nbsp; Serial numbering of old pucks
put this on Confluence

•&nbsp;&nbsp;&nbsp; Status of new puck order
One set (carousel) by March 3; we need to tell them when we need the next set.

•&nbsp;&nbsp;&nbsp; Order and manufacture of screens, frits, polysulfone
photofab gave too large holes so too weak.&nbsp; Laser cut would be more accurate.&nbsp; Give them (photofab) hard spec with feedback.&nbsp; Chris has info on the scintered frits and ordering specs.

{color:#ff0000}ACTION{color}:&nbsp; get inventory from Roman (Jim/Roman): laser-etch pore size for scintered frits

•&nbsp;&nbsp;&nbsp; Pressure pots ordered? Yes
•&nbsp;&nbsp;&nbsp; Status of 4K sphere:&nbsp; 2-piece pattern pictures sent to us: shipping them over to casting house

•&nbsp;&nbsp;&nbsp; Procurement schedule for next 2 cores

We don't have money from WHOI until late 2008.&nbsp; CMORE we're in the middle of that year

{color:#ff0000}ACTION{color}: discuss build schedule for next 2 cores at 1-24-2008 mtg (in two weeks).&nbsp;

h3. GUI Development

&nbsp;Kevin updated on GUI development.&nbsp; He would like to use his GUI tool to generate a mission-script for the Feb cold-room test.&nbsp; He needs reagent volumes to get accurate usage display.&nbsp; We will want to generate mission script the last week in January.&nbsp; Will meet tomorrow (Jan 11) to discuss volumes with him.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]]]></property>
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<property name="body"><![CDATA[h4. (as of Mar 28, 2013)


h3. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 day S. Cal ECOHAB w/ Bruce (Mar 2013)

*25.5m (bare)*

*25.3m (bare)*
* Catalina Island replacement (April 2014).&nbsp; Installed April 8.

*21.5m (w/ floats)*
* Catalina Island (April 2014).&nbsp; used for 21 days.&nbsp; Failed after 4.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'popped' when we opened it.&nbsp; Photo here.

*15.6m (w/ floats)*
* 35 day S. Cal ECOHAB w/Mack (Mar 2013)
* 41 day MB ECOHAB w/Mack (Sep 2013)

*15.2m (w/ floats)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h3. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]]]></property>
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<property name="body"><![CDATA[h4. (as of Mar 28, 2013)


h3. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 day S. Cal ECOHAB w/ Bruce (Mar 2013)

*25.5m (bare)*

*25.3m (bare)*
* Catalina Island replacement (April 2014).&nbsp; Installed April 8.

*21.5m (w/ floats)*
* Catalina Island (April 2014).&nbsp; used for 21 days.&nbsp; Failed after 4.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'popped' when we opened it.&nbsp; Photos [here|^Image 3.jpg|corrosion] and [here|^Image 2.jpg|salt crystals].

*15.6m (w/ floats)*
* 35 day S. Cal ECOHAB w/Mack (Mar 2013)
* 41 day MB ECOHAB w/Mack (Sep 2013)

*15.2m (w/ floats)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h3. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]]]></property>
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<property name="body"><![CDATA[Materials for Accel cartridge testing
# [Cartridge assembly document from Accel|^Cartage Assembly Procedure.docx|cartridge build procedure]
# [BOM for Cartridge (v1), puck, and holders|^BOM MBARI 2013-09-17.xlsx|BOM]

h2. +Test Plan v1&nbsp; (Sep 13, 2013)+

Must label ports/paths on cartridges

Convention for syringes (with spool valve on left) will be:
|| 0 || 1 \\ || 2 \\ || 3 \\ || 4 \\ ||
| Spool valve \\ | check valve | check valve \\ | | |
| | spring | spring | | |
| | air | RNALater | waste | waste \\ |
\\
\\

h5.


h4. Filtration Speed and Evac

\--22 PSI thru puck within CARTRIDGEwithin Accel Test Holder

within G2 holderusing raw seawater, with x3 replica's

h4. Syringe Functions

\--How to load syringes

\--check valves; do they leak or hold pressure?

\-After Final Assembly Testing by hand:
\--define actuation process

\--build bench testing actuator

h4. Full Assembly sub-test&nbsp; (all testing will have companion G2 comparison test)

&nbsp;--filter

\--move spool valve

\--evac w/ push

\--remove puck and weigh

When procedure refined, run w/ 0.45 filter and filter 'stacks'

h4. Final Assembly Test (all testing will have companion G2 comparison test)

&nbsp;--filter

\--move spool valve

\--evac w/ push

\--hit with RNALater

\--remove and process filter [BOM MBARI 2013-09-17 ARCHIVE CARTRIDGE.pdf|^BOM MBARI 2013-09-17 ARCHIVE CARTRIDGE.pdf|Cartridge v1 BOM]]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began

*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).
Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays
Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

MELO used was #300034012090780

location reported by MELO was-\- &nbsp; 33.4865 \-118.51285

*March 20*\--lost comms

*March 21*\--re-established comms and think problem in E/M cable.

*March 22*\--lost comms


h4. {color:#ff00cc}ECOHAB--S. California{color}]]></property>
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<property name="body"><![CDATA[h4. (as of Mar 28, 2013)


h3. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 day S. Cal ECOHAB w/ Bruce (Mar 2013)

*25.5m (bare)*

*25.3m (bare)*

*21.5m (w/ floats)*
* Catalina

*15.6m (w/ floats)*
* 35 day S. Cal ECOHAB w/Mack (Mar 2013)
* 41 day MB ECOHAB w/Mack (Sep 2013)

*15.2m (w/ floats)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h3. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]]]></property>
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<property name="body"><![CDATA[Email from Scott, January 9, 2008:&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), SH1(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; I need to confirm this list is exactly accurate.
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; The first set of snaps from El Camino shall be 1.&nbsp; The next set received from El Camino in March shall be 2 and the final group 3.
&nbsp;
I have started a spreadsheet that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;]]></property>
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<property name="spaceKey"><![CDATA[ESPAPP]]></property>
<property name="user"><![CDATA[jbirch]]></property>
<property name="creationDate">2008-01-03 08:56:17.177</property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://predator.shore.mbari.org/esp_gui/launch.jnlp]

h3. Project Documentation:

h3. Other Documents
# [Documents|ProjectDocuments]
# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
## [ESP GUI Demo and Questions|2007_09_05]
# [Presentations|ProjectPresentations]
# [Tasks]
# [Data Model]
# [Developer Documentation]

h3. Bug Tracking
# [JIRA Issue Tracker|http://oceana.shore.mbari.org:8082/browse/ESPAPP]

]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 10, 2008*

*10:30am-12*
Present:

h3.


h3. Tech Transfer

Action Items from last week:

ACTION: Brent will show Cheri and Addie how to read log (Brent & Cheri & Addie)
ACTION:&nbsp; run a sample on GG to compare pressures to NEO (Scott)
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)
ACTION: check with Jose and Tom about number of dwarves to order (Scott)
ACTION: discuss test box design with Jim Scholfield (Cheri)
ACTION:&nbsp; move connectors from 1K to the test box (Doug & Cheri)
ACTION: Clean B125 lab for CMORE visit (everyone)

Discussion Items:
•&nbsp;&nbsp;&nbsp; Surface can quote from IMT:&nbsp; 3 cans = \~$37K
•&nbsp;&nbsp;&nbsp; Mooring supplies for network deployment
•&nbsp;&nbsp;&nbsp; Update on test chamber and test chamber fixtures
•&nbsp;&nbsp;&nbsp; Arm status (see above)

h3. MFB

ACTION:&nbsp; Order custom valve heads (Addie)
ACTION:&nbsp; syringe motor mount.&nbsp; Mount 'upsidedown' for better lubrication.&nbsp; Changing motor for better gearing/speed ratio. (Addie)
ACTION:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (Scott/Brent/Addie)
ACTION:&nbsp; Sleepy board given to Brent, w/ Addie using a dwarf board (Addie)
ACTION:&nbsp; talk to Tony and get timeline on next MFB (Jim)

Discussion Items:
•&nbsp;&nbsp;&nbsp; LLNL schedule---Tony coming Jan. 23.
•&nbsp;&nbsp;&nbsp; Syringe lubrication
•&nbsp;&nbsp;&nbsp; Mixing column for extraction lysate.&nbsp; Discuss construction.

h3. Software

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)
ACTION:&nbsp; change laptops and ARM boards and install the new Ruby interpreter (Brent)
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent)
ACTION:&nbsp; Work with the auto-cal code (Brent)
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim)

Discussion Items:
•&nbsp;&nbsp;&nbsp; Sampling technique.&nbsp; Greater pressure or 'pulsing' or both?
•&nbsp;&nbsp;&nbsp; Themal control hardware.&nbsp; Necessitate a firmware change?
•&nbsp;&nbsp;&nbsp; Modification of friction compensation w/in servo code.
•&nbsp;&nbsp;&nbsp; Other software changes and test plan for their implementation

h3. Sphere and 4K DWSMS

ACTION:&nbsp; Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott).&nbsp; Still be to done.
ACTION:&nbsp; Buy two boxes, populate with D-cells.&nbsp; One with lead-acid will remain lead-acid. (Scott) Jim get account # to charge.
ACTION: will try and have model done by end of Jan--depends on pumps (Doug)
ACTION: Get quote for surface cans from Gene and place order (Jim)
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04

Discussion Items:
•&nbsp;&nbsp;&nbsp; Serial numbering of old pucks
•&nbsp;&nbsp;&nbsp; Status of new puck order
•&nbsp;&nbsp;&nbsp; Order and manufacture of screens, frits, polysulfone
•&nbsp;&nbsp;&nbsp; Pressure pots ordered?
•&nbsp;&nbsp;&nbsp; Status of 4K sphere
•&nbsp;&nbsp;&nbsp; Status of plastic DWSM development
•&nbsp;&nbsp;&nbsp; Procurement schedule for next 2 cores
o&nbsp;&nbsp;&nbsp; WHOI---core delivery Summer 2009
o&nbsp;&nbsp;&nbsp; CMORE---start build in 2008

Surface Expression:&nbsp; who has plans?&nbsp;

h3.

On Table:

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 10, 2008*

*10:30am-12*
Present:&nbsp; Jim, Chris S., Brent, Doug, Kevin G,

After today meetings will be 11-12&nbsp;

h3.


h3. Tech Transfer

Action Items from last week:

ACTION: Brent will show Cheri and Addie how to read log (Brent & Cheri & Addie)&nbsp; DONE
ACTION:&nbsp; run a sample on GG to compare pressures to NEO (Scott)&nbsp; DONE
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; Not done
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; Not Done
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; Not Done
ACTION: check with Jose and Tom about number of dwarves to order (Scott)&nbsp; Jose still diggin through BOM to figure out what we can order&nbsp; (1/4 way through)
ACTION: discuss test box design with Jim Scholfield (Cheri)&nbsp; Jim and Cheri and Scott discussed design; he's ordering parts.&nbsp; Maybe endo of next.
ACTION:&nbsp; move connectors from 1K to the test box (Doug & Cheri)&nbsp; Been pulledoff 1K and now at Jim S (electrical).&nbsp; Fuildic we are going to use ones that Mike made.&nbsp; Doug things theyare in lab downstairs.
ACTION: Clean B125 lab for CMORE visit (everyone)

Discussion Items:
•&nbsp;&nbsp;&nbsp; Surface can quote from IMT:&nbsp; 3 cans = \~$37K

cannot purchase on 708 grant yet.&nbsp; 701312.04 should take all cost.

•&nbsp;&nbsp;&nbsp; Mooring supplies for network deployment

No one knows everything.&nbsp; We can get by with 2, but we really need 3.&nbsp; Doug says it's 6 months of Jim S. time, but Chris thought 1 month.

We have 2 complete moorings.

ACTION:&nbsp; confirm we have 3 swapable EM cables and purchase spares for 701312.04 including labor


•&nbsp;&nbsp;&nbsp; Update on test chamber and test chamber fixtures
•&nbsp;&nbsp;&nbsp; Arm status (see above)

h3. MFB

ACTION:&nbsp; Order custom valve heads (Addie)&nbsp; DONE
ACTION:&nbsp; syringe motor mount.&nbsp; Mount 'upsidedown' for better lubrication.&nbsp; Changing motor for better gearing/speed ratio. (Addie)&nbsp; SEE BELOW
ACTION:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (Scott/Brent/Addie):&nbsp; DONE
ACTION:&nbsp; Sleepy board given to Brent, w/ Addie using a dwarf board (Addie):&nbsp; DONE
ACTION:&nbsp; talk to Tony and get timeline on next MFB (Jim):&nbsp; DONE

Discussion Items:
•&nbsp;&nbsp;&nbsp; LLNL schedule---Tony coming Jan. 23.&nbsp; DONE

ACTION: confirm with email to Tony (Jim)

•&nbsp;&nbsp;&nbsp; Syringe lubrication

Syringe motor is changed to higher encoder one.&nbsp; Should be no problem to get slower speed; pin numbers were different (10 new vs 6 old).&nbsp; Brent and Addie working on aligning it.&nbsp; Config file is now cleaned and only contains MFB stuff.&nbsp; Flipping syringe will allow lube to sit on top of plunger.&nbsp; Syringe will be flipped.

•&nbsp;&nbsp;&nbsp; Mixing column for extraction lysate.&nbsp; Discuss construction.

Cannot put PEEK 2ml ID tubing into our smaller fittings.&nbsp; But can use 1/4-28 fitting normally.&nbsp; So Addie instructed to build simply stand-pipe structure with PEEK.&nbsp; May look at Optimize.com who make HPLC mixing chambers to see if they have these chambers. Addie going to check out standpipe

h3. Software

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)
ACTION:&nbsp; change laptops and ARM boards and install the new Ruby interpreter (Brent)
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent)
ACTION:&nbsp; Work with the auto-cal code (Brent)
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim)

Discussion Items:
•&nbsp;&nbsp;&nbsp; Sampling technique.&nbsp; Greater pressure or 'pulsing' or both?
•&nbsp;&nbsp;&nbsp; Themal control hardware.&nbsp; Necessitate a firmware change?
•&nbsp;&nbsp;&nbsp; Modification of friction compensation w/in servo code.
•&nbsp;&nbsp;&nbsp; Other software changes and test plan for their implementation

h3. Sphere and 4K DWSMS

ACTION:&nbsp; Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott).&nbsp; Still be to done.
ACTION:&nbsp; Buy two boxes, populate with D-cells.&nbsp; One with lead-acid will remain lead-acid. (Scott) Jim get account # to charge.
ACTION: will try and have model done by end of Jan--depends on pumps (Doug)
ACTION: Get quote for surface cans from Gene and place order (Jim)
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04

Discussion Items:
•&nbsp;&nbsp;&nbsp; Serial numbering of old pucks
•&nbsp;&nbsp;&nbsp; Status of new puck order
•&nbsp;&nbsp;&nbsp; Order and manufacture of screens, frits, polysulfone
•&nbsp;&nbsp;&nbsp; Pressure pots ordered?
•&nbsp;&nbsp;&nbsp; Status of 4K sphere
•&nbsp;&nbsp;&nbsp; Status of plastic DWSM development
•&nbsp;&nbsp;&nbsp; Procurement schedule for next 2 cores
o&nbsp;&nbsp;&nbsp; WHOI---core delivery Summer 2009
o&nbsp;&nbsp;&nbsp; CMORE---start build in 2008

Surface Expression:&nbsp; who has plans?&nbsp;

h3.

On Table:

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 10, 2008*

*10:30am-12*
Present:&nbsp; Jim, Chris S., Brent, Doug, Kevin G,

After today meetings will be 11-12&nbsp;

h3.


h3. Tech Transfer

Action Items from last week:

ACTION: Brent will show Cheri and Addie how to read log (Brent & Cheri & Addie)&nbsp; DONE
ACTION:&nbsp; run a sample on GG to compare pressures to NEO (Scott)&nbsp; DONE
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; Not done
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; Not Done
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; Not Done
ACTION: check with Jose and Tom about number of dwarves to order (Scott)&nbsp; Jose still diggin through BOM to figure out what we can order&nbsp; (1/4 way through)
ACTION: discuss test box design with Jim Scholfield (Cheri)&nbsp; Jim and Cheri and Scott discussed design; he's ordering parts.&nbsp; Maybe endo of next.
ACTION:&nbsp; move connectors from 1K to the test box (Doug & Cheri)&nbsp; Been pulledoff 1K and now at Jim S (electrical).&nbsp; Fuildic we are going to use ones that Mike made.&nbsp; Doug things theyare in lab downstairs.
ACTION: Clean B125 lab for CMORE visit (everyone)

Discussion Items:
•&nbsp;&nbsp;&nbsp; Surface can quote from IMT:&nbsp; 3 cans = \~$37K

ACTION:&nbsp; cannot purchase on 708 grant yet.&nbsp; 701312.04 should take all cost.&nbsp; Change:&nbsp; Order only 2 cans


•&nbsp;&nbsp;&nbsp; Mooring supplies for network deployment

No one knows everything.&nbsp; We can get by with 2, but we really need 3.&nbsp; Doug says it's 6 months of Jim S. time, but Chris thought 1 month.

We have 2 complete moorings.

ACTION:&nbsp; confirm we have 3 swapable EM cables and purchase spares from 701312.04 (including labor).

•&nbsp;&nbsp;&nbsp; Update on test chamber and test chamber fixtures


•&nbsp;&nbsp;&nbsp; Arm status (see above)

Assembly issue on arm caused binding which is what caused failure last week.&nbsp; Reassmbly found broken wires in home sensor.&nbsp; Friday was working great at 10 degrees all weekend.&nbsp; Checked Monday morning it looked fine.&nbsp; Lowered temp to 2C and Tuesday found ribbon cable home sensor cable was broken.&nbsp; There is a loop for a strain relief.&nbsp; Brent suggests mylar cable used in printer.&nbsp; Chris suggests a 'ticker' to count cycles so we know when things should be changed.&nbsp; Revalving has started on Mack; 7 of 8 have been done.&nbsp; Modifying mount on 8th one.&nbsp; Should be done by Monday.

We will use 'non-ideal' arms for Spring deployment, but when we order new hands, we will order the correct ones.&nbsp;

ACTION:&nbsp; talk to Jose to figure a solution to this problem. &nbsp; (Scott/Doug/Cheri)

ACTION: Contact MAXON about forearm motors (Cheri)&nbsp;

h3. MFB

ACTION:&nbsp; Order custom valve heads (Addie)&nbsp; DONE
ACTION:&nbsp; syringe motor mount.&nbsp; Mount 'upsidedown' for better lubrication.&nbsp; Changing motor for better gearing/speed ratio. (Addie)&nbsp; SEE BELOW
ACTION:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (Scott/Brent/Addie):&nbsp; DONE
ACTION:&nbsp; Sleepy board given to Brent, w/ Addie using a dwarf board (Addie):&nbsp; DONE
ACTION:&nbsp; talk to Tony and get timeline on next MFB (Jim):&nbsp; DONE

Discussion Items:
•&nbsp;&nbsp;&nbsp; LLNL schedule---Tony coming Jan. 23.&nbsp; DONE

ACTION: confirm with email to Tony (Jim)

•&nbsp;&nbsp;&nbsp; Syringe lubrication

Syringe motor is changed to higher encoder one.&nbsp; Should be no problem to get slower speed; pin numbers were different (10 new vs 6 old).&nbsp; Brent and Addie working on aligning it.&nbsp; Config file is now cleaned and only contains MFB stuff.&nbsp; Flipping syringe will allow lube to sit on top of plunger.&nbsp; Syringe will be flipped.

•&nbsp;&nbsp;&nbsp; Mixing column for extraction lysate.&nbsp; Discuss construction.

Cannot put PEEK 2ml ID tubing into our smaller fittings.&nbsp; But can use 1/4-28 fitting normally.&nbsp; So Addie instructed to build simply stand-pipe structure with PEEK.&nbsp; May look at Optimize.com who make HPLC mixing chambers to see if they have these chambers. Addie going to check out standpipe

h3. Software

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; Can't find elmo but have other pieces.
ACTION:&nbsp; change laptops and ARM boards and install the new Ruby interpreter (Brent):&nbsp; DONE
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): Nope
ACTION:&nbsp; Work with the auto-cal code (Brent):&nbsp; Nope
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): Wayne still on vacation


Discussion Items:
•&nbsp;&nbsp;&nbsp; Sampling technique.&nbsp; Greater pressure or 'pulsing' or both?

Brent has maxed the vacuum in the syringe without cavitation.&nbsp; Chris can provide natural sample.&nbsp; To get more sample volume do we want to experiemnt with a greater deltaP?&nbsp;


ACTION:&nbsp; Chris to give Brent water sample for running next week.&nbsp; Test running on bench at various pressures and run lysate test to test effects of different pressures (Chris/Brent)&nbsp;


•&nbsp;&nbsp;&nbsp; Themal control hardware.&nbsp; Necessitate a firmware change?

Scott has a new sensor setup.&nbsp; Goal would be to eliminate funny ramps in RUBY to avoid overshooting.&nbsp; These controls are already in the DC motor controllers, so should we use this control in the temp control?&nbsp; Worry is it's a big change.&nbsp; Firmware/Ruby must both change.&nbsp; This started because we don't get to that temperature; its a function of ambient in the can.&nbsp; Chris; if offset is pretty well known, then we could live with it, if offset is big, it could screw up our array results.&nbsp; We can change the hardware, but getting software changed over may take too long.

ACTION:&nbsp; Will change the hardware, look at offsets (Scott)

This will dictate next step.&nbsp;


•&nbsp;&nbsp;&nbsp; Modification of friction compensation w/in servo code.

In progress, but not as important as heating offsets.


•&nbsp;&nbsp;&nbsp; Other software changes and test plan for their implementation

Test pressure stuff; if problems, then heating stuff is dropped&nbsp;

h3. Sphere and 4K DWSMS

ACTION:&nbsp; Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott).&nbsp; Still be to done.

Get Nilo to take lead on this with Roman oversight.


ACTION:&nbsp; Buy two boxes, populate with D-cells.&nbsp; One with lead-acid will remain lead-acid. (Scott) Jim get account # to charge. NSF creativity
ACTION: will try and have model done by end of Jan--depends on pumps (Doug)

Can readily put together plastic housing.&nbsp; Still working on type of pumps
ACTION: Get quote for surface cans from Gene and place order (Jim):&nbsp; Done
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: Scott waiting for lower price


Discussion Items:
•&nbsp;&nbsp;&nbsp; Serial numbering of old pucks

put this on Confluence
•&nbsp;&nbsp;&nbsp; Status of new puck order

One set (carousel) by March 3; we need to tell them when we need the next set.
•&nbsp;&nbsp;&nbsp; Order and manufacture of screens, frits, polysulfone

photofab gave too large holes so too weak.&nbsp; Laser cut would be more accurate.&nbsp; Give them (photofab) hard spec with feedback.&nbsp; Chris has info on the scintered frits and ordering specs.


ACTION:&nbsp; get inventory from Roman (Jim/Roman): laser-etch pore size for scintered frits
•&nbsp;&nbsp;&nbsp; Pressure pots ordered? Yes
•&nbsp;&nbsp;&nbsp; Status of 4K sphere:&nbsp; 2-piece pattern pictures sent to us: shipping them over to casting house
•&nbsp;&nbsp;&nbsp; Status of plastic DWSM development
•&nbsp;&nbsp;&nbsp; Procurement schedule for next 2 cores

We don't have money from WHOI until late 2008.&nbsp; CMORE we're in the middle of that year

discuss build schedule in two weeks.&nbsp;


o&nbsp;&nbsp;&nbsp; WHOI---core delivery Summer 2009
o&nbsp;&nbsp;&nbsp; CMORE---start build in 2008

Surface Expression:&nbsp; who has plans?&nbsp;

h3.

On Table:

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)

GUI development:&nbsp; kevin update.&nbsp; Take GUI tool to generate the trial-mission script for Feb cold-room test.&nbsp; Kevin needs volumes of reagents to allow usage display.

last week in Jan we will want to generate the mission script.&nbsp; Should get together the week before to verify volumes.&nbsp; Will meet tomorrow afternoon for this. &nbsp;&nbsp;]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/fluid%20worksheet%20MFB%2014-MAR-07.pdf]
# [Engineering Timeline]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]

h2. Science]]></property>
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<property name="body"><![CDATA[h3. Deployments as they happened:

April 3&nbsp;&nbsp;  &nbsp;&nbsp;  Deploy Mack (M0)
April 21&nbsp;&nbsp;&nbsp; Recover Mack&nbsp;
\\

May 1&nbsp;&nbsp;&nbsp; Deploy Mack (M0)
May 12&nbsp;&nbsp;&nbsp; Mack craps out (syringe sticking)
May 15&nbsp;&nbsp;&nbsp; Recover Mack and can swap with Bruce

{color:#ff0000}{*}Plan:*{color}
May 27&nbsp;&nbsp;&nbsp; Recover Bruce
May 28&nbsp;&nbsp;&nbsp; Deploy Mack and Neo (SC and M0)&nbsp;]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables]
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
# [2014 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h4. (as of Mar 28, 2013)


h3. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 day S. Cal ECOHAB w/ Bruce (Mar 2013)

*25.5m (bare)*

*25.3m (bare)*

*21.5m (w/ floats)*
* Catalina

*15.6m (w/ floats)*
* 35 day S. Cal ECOHAB w/Mack (Mar 2013)
* 41 day MB ECOHAB w/Mack (Sep 2013)

*15.2m (w/ floats)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h3. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them. ]]></property>
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<property name="body"><![CDATA[h4. (as of Mar 28, 2013)


h3. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 day S. Cal ECOHAB w/ Bruce (Mar 2013)

*25.5m (bare)*

*25.3m (bare)*

*21.5m (w/ floats)*
* Catalina

*15.6m (w/ floats)*
* 35 day S. Cal ECOHAB w/Mack (Mar 2013)
* 41 day MB ECOHAB w/Mack (Sep 2013)

*15.2m (w/ floats)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h3. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h3. [shockle-line lengths.xlsx|^shockle-line lengths.xlsx|lengths .xls]]]></property>
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<property name="body"><![CDATA[Present: Jim, Brent, Scott, Addie, Doug, Cheri
Absent: Kevin, Wayne, Chris S.&nbsp;

h3. Instrument Builds/Tech Transfer

* South Carolina person here {color:#ff0000}August 21-29{color} to run Mack & Bruce (Tina Mukulsky (sp?))
* Bruce temp calibrations finished and verified.&nbsp; Mack will be finished by the end of today.
* Roman will help with verification check.
* Wiring harnesses for CMORE/NSF/Moe are in and being QC'd.&nbsp; Will wait to order MFB harnesses when grill layout is finalized.
* Gripper board and puck sensor boards have very slight redesigns.&nbsp; Still waiting to determine how many of each to make, and whether we should switch out current machines with new redesigned boards.

h3. MFB

* motors on grill working, but encoders not.&nbsp; (FRIDAY update:&nbsp; encoders now working)
* We must come up with naming convention of the MFB's for accessing via software.
* Will daisy-chain power from SPE to PCR module.
* Serial connection from PCR to either host card or a laptop.
* Much discussion of whether to include a host card on each MFB.&nbsp; Without the card, stand-alone MFB's will require laptop to run; they would be unaffected when attached to the core.&nbsp; While it may impact low-level software development to have a host-card on each MFB, the simplicity of a _complete_ stand-alone unit for the external user dictates mounting a host card.
* We must build several Power Boards; will populate here at MBARI (Scott)
* Closed-cell foam being explored for insulating the SPE block

h3. Software

* Brent has 2 radios working simultaneously; working on adding a third.
* Second in priority is the limit-switch testing, a critical path item for DWSM
* At LINUX expo, Brent talked to people about putting WiFi on mooring, good for 7-8 miles los.&nbsp; We should explore; perhaps contingency project in 2009 for Brent.
* Antenna lease agreement finished and out for comment.&nbsp; We will need to purchase serial cable to connect house to radio.

h3. DWSM

* Sphere update--We have had conference call to Tapemeation.&nbsp; They expect to get spheres on lathe in 4 weeks, completed by end of October.
* Ti screws might be very expensive for the size we want.&nbsp; Doug exploring helicoils as good alternative.&nbsp; Decision needs to be made before Tapemation begins machining.
* Bell Housing needed slight modification since part ordered by El Camino was too short.&nbsp; Other parts are now in machine shopl
* Doug wants to try and do swiss cheese plate in-house.
* Most COTS parts are here--still need Mini-Con's, Swageloc, various connectors/cables
* Electronics--Boards laid out;&nbsp; Scott wants miniEE review late next week
* Note about elevator assembly-\- want to be able to open and 'get at' sphere
* &nbsp;
* &nbsp;

h3. Other Items

* Kevin estimates $10K for machine-state visualization software
* Brent wants to test limit switches--can do w/ stuff on his desk
* Still must do radio test--configuration with 3 radios
* Brent found another antenna place
** we will draw up a 'contract' detaling time, it's our stuff, we'd pay for his cable, give notice of renewal--Jim to work with Brent on this.]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]]]></property>
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<property name="body"><![CDATA[h1. Meeting to discuss ESP Phases, Protocol Runs, and Consumables


h3. Attendees:

# Kevin Gomes
# Roman Marin
# Jim Birch

h3. Agenda

The focus of this meeting is to identify all the appropriate phases, protocol runs and consumables and their amounts (recipies) that will be available for planning a mission on an ESP instrument.

h3. List from previous meeting


h5. Instruments:

# NEO

h5. Lists of phases, protocols

# HAB
## SH1
## lyfil
## SH2
## WCR
# DA
## DA1
## Dalyfil
## DA2
# BAC
## SH1
## lyfil
## SH2
## WCR
# invert
## SH1
## lyfil
## SH2
## WCR
# BACAR
## WCR
# QC
## WCR

h5. Details for phases:

# Max duration

h5. Details for protocols:

# Duration
# Delay to sample

h5. Consumable Types:

# Fix
# AgMeOH
# ab1
# ab2
# Lysis
# Dilutent
# Sig1
# Sig2
# Sig3
# Con 1:5000
# Sub 1
# Sub 2
# Wash
# CSR Flush
# CSV Flush
# PSR Flush
# Kill
# Waste
# Power

h5. Bags/Containers/Storage:

# For NEO, how big are the capacities for the above consumables?

h5. Protocol/Consumable Details (for each of the phase/protocol combination, what consumables do they use and how much?)

# Excel Spreadsheet?

h5. Mission Script Syntax (Work with Brent Roman)]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began

*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).
Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays
Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

MELO used was #300034012090780

location reported by MELO was-\- &nbsp; 33.4865 \-118.51285


h4. {color:#ff00cc}ECOHAB--S. California{color}]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began

*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).
Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays
Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

MELO used was #300034012090780

location reported by MELO was-\- &nbsp; 33.4865 \-118.51285

*March 20*\--lost comms

*March 21*\--re-established comms and s

h4. {color:#ff00cc}ECOHAB--S. California{color}]]></property>
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<property name="body"><![CDATA[h1. Meeting to discuss ESP Phases, Protocol Runs, and Consumables

h3. Attendees:
# Kevin Gomes

h3. Agenda
The focus of this meeting is to identify all the appropriate phases, protocol runs and consumables and their amounts (recipies) that will be available for planning a mission on an ESP instrument.

h3. List from previous meeting
h5. Instruments:
# NEO

h5. Lists of phases, protocols
# HAB
## SH1
## lyfil
## SH2
## WCR
# DA
## DA1
## Dalyfil
## DA2
# BAC
## SH1
## lyfil
## SH2
## WCR
# invert
## SH1
## lyfil
## SH2
## WCR
# BACAR
## WCR
# QC
## WCR

h5. Details for phases:
# Max duration

h5. Details for protocols:
# Duration
# Delay to sample

h5. Consumable Types:
# Fix
# AgMeOH
# ab1
# ab2
# Lysis
# Dilutent
# Sig1
# Sig2
# Sig3
# Con 1:5000
# Sub 1
# Sub 2
# Wash
# CSR Flush
# CSV Flush
# PSR Flush
# Kill
# Waste
# Power

h5. Bags/Containers/Storage:
# For NEO, how big are the capacities for the above consumables?

h5. Protocol/Consumable Details (for each of the phase/protocol combination, what consumables do they use and how much?)
# Excel Spreadsheet?

h5. Mission Script Syntax (Work with Brent Roman)
]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)]]></property>
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<property name="body"><![CDATA[h1. Meeting to discuss ESP Phases, Protocol Runs, and Consumables


h3. Attendees:

# Kevin Gomes
# Roman Marin
# Jim Birch
# Chris Preston

h3. Agenda

The focus of this meeting is to identify all the appropriate phases, protocol runs and consumables and their amounts (recipies) that will be available for planning a mission on an ESP instrument.

h3. List from previous meeting


h5. Instruments:

# NEO
# GIGI

h5. Lists of phases, protocols

# HAB
## SH1
## lyfil
## SH2
## WCR
# DA
## DA1
## Dalyfil
## DA2
# BAC
## SH1
## lyfil
## SH2
## WCR
# invert
## SH1
## lyfil
## SH2
## WCR
# BACAR
## WCR
# QC
## WCR

h5. Details for phases:

# Max duration

h5. Details for protocols:

# Duration
# Delay to sample

h5. Consumable Types:

# Fix
# AgMeOH
# ab1
# ab2
# Lysis
# Dilutent
# Sig1
# Sig2
# Sig3
# Con 1:5000
# Sub 1
# Sub 2
# Wash
# CSR Flush
# CSV Flush
# PSR Flush
# Kill
# Waste
# Power

h5. Bags/Containers/Storage:

# For NEO, how big are the capacities for the above consumables?

h5. Protocol/Consumable Details (for each of the phase/protocol combination, what consumables do they use and how much?)

# Excel Spreadsheet?

h5. Mission Script Syntax (Work with Brent Roman)]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://ssdsmac.shore.mbari.org/esp_gui/launch.jnlp]

h3. Project Documentation:

h3. Other Documents
# [Documents|Documents Related to GUI Component]
# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
## [ESP GUI Demo and Questions|2007_09_05]
## [Follow up meeting on Resources and Consumables|2008_01_08]
## [Mock Mission Planning Meeting|2008_03_11]
# [Presentations|ProjectPresentations]
# [Data Model]
# [Developer Documentation]

h3. Bug Tracking
# [JIRA Issue Tracker|https://oceana.mbari.org/jira/browse/ESPII]

]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://predator.shore.mbari.org/esp_gui/launch.jnlp]

h3. Project Documentation:

h3. Other Documents
# [Documents|Documents Related to GUI Component]
# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
## [ESP GUI Demo and Questions|2007_09_05]
## [Follow up meeting on Resources and Consumables|2008_01_08]
## [Mock Mission Planning Meeting|2008_03_11]
# [Presentations|ProjectPresentations]
# [Data Model]
# [Developer Documentation]

h3. Bug Tracking
# [JIRA Issue Tracker|https://oceana.mbari.org/jira/browse/ESPII]

]]></property>
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<property name="body"><![CDATA[Doug will be on vacation July 14-July 28.



present:


h3. Instrument Builds


h3. MFB


h3. Software


h3. Other Items]]></property>
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<property name="body"><![CDATA[h4. (as of Mar 28, 2013)


h3. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 day S. Cal ECOHAB w/ Bruce (Mar 2013)

*25.5m (bare)*

*25.3m (bare)*

*21.5m (w/ floats)*

*15.6m (w/ floats)*
* 35 day S. Cal ECOHAB w/Mack (Mar 2013)
* 41 day MB ECOHAB w/Mack (Sep 2013)

*15.2m (w/ floats)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h3. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them. ]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 10, 2008*

*10:30am-12*
Present:

h3.


h3. Tech Transfer

Action Items from last week:

ACTION: Brent will show Cheri and Addie how to read log (Brent & Cheri & Addie)
ACTION:&nbsp; run a sample on GG to compare pressures to NEO (Scott)
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)
ACTION: check with Jose and Tom about number of dwarves to order (Scott)
ACTION: discuss test box design with Jim Scholfield (Cheri)
ACTION:&nbsp; move connectors from 1K to the test box (Doug & Cheri)
ACTION: Clean B125 lab for CMORE visit (everyone)

Discussion Items:
•&nbsp;&nbsp;&nbsp; Surface can quote from IMT:&nbsp; 3 cans = \~$37K
•&nbsp;&nbsp;&nbsp; Mooring supplies for network deployment
•&nbsp;&nbsp;&nbsp; Update on test chamber and test chamber fixtures
•&nbsp;&nbsp;&nbsp; Arm status (see above)



h3. MFB

ACTION:&nbsp; Order custom valve heads (Addie)
ACTION:&nbsp; syringe motor mount.&nbsp; Mount 'upsidedown' for better lubrication.&nbsp; Changing motor for better gearing/speed ratio. (Addie)
ACTION:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (Scott/Brent/Addie)
ACTION:&nbsp; Sleepy board given to Brent, w/ Addie using a dwarf board (Addie)
ACTION:&nbsp; talk to Tony and get timeline on next MFB (Jim)

Discussion Items:
•&nbsp;&nbsp;&nbsp; LLNL schedule---Tony coming Jan. 23.
•&nbsp;&nbsp;&nbsp; Syringe lubrication
•&nbsp;&nbsp;&nbsp; Mixing column for extraction lysate.&nbsp; Discuss construction.



h3. Software

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)
ACTION:&nbsp; change laptops and ARM boards and install the new Ruby interpreter (Brent)
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent)
ACTION:&nbsp; Work with the auto-cal code (Brent)
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim)

Discussion Items:
•&nbsp;&nbsp;&nbsp; Sampling technique.&nbsp; Greater pressure or 'pulsing' or both?
•&nbsp;&nbsp;&nbsp; Themal control hardware.&nbsp; Necessitate a firmware change?
•&nbsp;&nbsp;&nbsp; Modification of friction compensation w/in servo code.
•&nbsp;&nbsp;&nbsp; Other software changes and test plan for their implementation


h3. Sphere and 4K DWSMS

ACTION:&nbsp; Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott).&nbsp; Still be to done.
ACTION:&nbsp; Buy two boxes, populate with D-cells.&nbsp; One with lead-acid will remain lead-acid. (Scott) Jim get account # to charge.
ACTION: will try and have model done by end of Jan--depends on pumps (Doug)
ACTION: Get quote for surface cans from Gene and place order (Jim)
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04

Discussion Items:
•&nbsp;&nbsp;&nbsp; Serial numbering of old pucks
•&nbsp;&nbsp;&nbsp; Status of new puck order
•&nbsp;&nbsp;&nbsp; Order and manufacture of screens, frits, polysulfone
•&nbsp;&nbsp;&nbsp; Pressure pots ordered?
•&nbsp;&nbsp;&nbsp; Status of 4K sphere
•&nbsp;&nbsp;&nbsp; Status of plastic DWSM development
•&nbsp;&nbsp;&nbsp; Procurement schedule for next 2 cores
o&nbsp;&nbsp;&nbsp; WHOI---core delivery Summer 2009
o&nbsp;&nbsp;&nbsp; CMORE---start build in 2008


h3.
On Table:

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 10, 2008*

*10:30am-12*
Present:


h3. *Tech Transfer*

•&nbsp;&nbsp; &nbsp;Cheri; plan for hand cold-testing/re-valving by Jan 15

Bruce in chamber on Monday and running a shuffle (looped).&nbsp; It had stopped with forearm errors.&nbsp; Brent will help find when/why crashed.&nbsp; Restarted shuffle on Weds, but after awhile if gets worse and worse and stops.&nbsp; Does it both in cold and at room temp.&nbsp;

{color:#ff0000}ACTION:{color} Brent will show Cheri and Addie how to read log ({color:#0000ff}Brent & Cheri & Addie{color})

•&nbsp;&nbsp; &nbsp;Status of slow-running intake on GG

GG's pressure sensor broken.&nbsp; Found that the clamp holes were too small, and installation torqued the sensors so they were wrongly calibrated. Our fix is was to recalibrate when clamps are pressurized, but this masked the&nbsp; real problem.&nbsp; Not that pressure sensor mounting holes are correct, must run a sample on GG to see if it's smilar to NEO.

{color:#ff0000}ACTION:{color}&nbsp; run a sample on GG to compare to NEO ({color:#3300ff}Scott{color})

•&nbsp;&nbsp; &nbsp;Status of manipulator hands

Have one hand but lots of calibration issues.&nbsp; Parts for other two hands still on hold until first one works.&nbsp; Mike currently working on valve motor mounts and gears.&nbsp;

{color:#ff0000}ACTION{color}:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly ({color:#0000ff}Scott{color})

Will get one hand working then build 3 more.&nbsp; Cheri discussed the design of the linkage which make the hands not move together when they close.&nbsp; Currently all arms are the same (non-ideal) design.

{color:#ff0000}ACTION{color}:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands ({color:#0000ff}Doug{color})&nbsp;

•&nbsp;&nbsp; &nbsp;Drill out pressure sensor holes in clamps

{color:#ff0000}ACTION{color}: Will do this when we revalve the cores. ({color:#0000ff}Scott/Cheri{color})

•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?
sent an email but nothing back from company...
{color:#ff0000}ACTION{color}: call and find out where the company is in development ({color:#0000ff}Scott{color})

•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?
Jose adding up inventory.&nbsp; We will need enough for 2 cores and 8 MFBs and spares (at least 1 full core and enough spares for 8 MFB's\[3 dwarves, 2 R's\]).&nbsp; Tally up, look at production run, and scale up for best economy.&nbsp; Will place order early January.

{color:#ff0000}ACTION{color}: check with Jose and&nbsp; Tom ({color:#0000ff}Scott{color})

*•&nbsp;&nbsp; &nbsp;CMORE workshop Jan. 14-17*;&nbsp;
* roll-up core and MFB to Pacific Forum
* clean B125 lab
* clean up MFB (get rid of sleepy/medusa of wires/tubes, have a 'show' script)

Will take sleepy off MFB and give to Brent and substitute with dwarf, and Addie will work on cleaning and gussing up MFB

h4. Final Tech Transfer Issues

The plastic chamber box; should be as near the volume of the cylinder as possible.&nbsp; Will not be using endcap since it doesn't fit.&nbsp; Talk to Jim S. to build the&nbsp; box.

Connectors; have researched how to populate the lid--only one power, ethernet, console, contextual sensors (3), modem, external sampler.&nbsp; Will remove these from the 1K housing.

{color:#ff0000}ACTION{color}:&nbsp; move connectors from 1K to the test box ({color:#0000ff}Doug & Cher{color}i)
\\

h3. *MFB*

* Update on solid Phase Extraction.&nbsp; Protocol development?

SPE working well now.&nbsp; Further protocol refinements will&nbsp; wait until Chris P. has submitted her paper.&nbsp;
* place order with MAXON for MFB spares (Addie)

Ordered.&nbsp; just need the PO approved.&nbsp; 6-8 week lead time.&nbsp;
* Update on PSV valve addition and connection w/ core
* &nbsp;Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addie will figure out how to connect ports 3, 5, 6 with no bubbles. (Addie).&nbsp; They have been called; waiting for response.

•&nbsp;&nbsp; &nbsp;Report on syringe lubrication.&nbsp; Success?

Has lubed it several times, but still getting trajectory errors.&nbsp; The motor is at the edge of it's capability (moving almost TOO slowly).&nbsp; Addie has 2-3 motors with bigger gear box, 2-3 with better encoder, and 2-3 with both.

{color:#ff0000}ACTION{color}:&nbsp; will try many of these motors, then work on flipping. Must get to the slow speed of 1ul/sec. ({color:#0000ff}Addie{color})&nbsp;

{color:#ff0000}ACTION{color}:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this ({color:#0000ff}Scott/Brent/Addie{color})

There was discussion of running our reagents out at LLNL to see if we can emulate their results, but with our reagents.&nbsp; Will discuss with LLNL.

{color:#ff0000}ACTION{color}:&nbsp; talk to Tony and get timeline on next MFB ({color:#0000ff}Jim{color})&nbsp;

h3. *Software*

•&nbsp;&nbsp; &nbsp;Status of current Ruby version.&nbsp; Close to lock-down?

Brent has written a fix that is more efficient when bouncing between threads.&nbsp; So no garbage collection issues now.&nbsp; Was unable to recreate the error with DWSM, but found a problem with driving the I2C bus with a fast laptop--maybe something related to how quickly data is driven to the serial command bus.&nbsp;&nbsp;

Ruby interpreter is stable for this year.&nbsp; As close to 'frozen' that we'll get.&nbsp;

{color:#ff0000}ACTION{color}: Set-up sleepy board and an elmo on desk to emulate ({color:#0000ff}Brent{color})

{color:#ff0000}ACTION{color}:&nbsp; change laptops and ARM boards and install the new Ruby interpreter ({color:#0000ff}Brent{color})

{color:#ff0000}ACTION{color}:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] ({color:#0000ff}Brent{color})

{color:#ff0000}ACTION{color}:&nbsp; Work with the auto-cal code ({color:#0000ff}Brent{color})

•&nbsp;&nbsp; &nbsp;Issues for Wayne:
o&nbsp;&nbsp; &nbsp;Low power CPU replacement
o&nbsp;&nbsp; &nbsp;USB camera porting from Kernel 2.4 to Kernel 2.6
o&nbsp;&nbsp; &nbsp;Improve dwarve DC servo control algorithm
o&nbsp;&nbsp; &nbsp;Improve ESP hardware simulator (Ruby)

Low power CPU being put off until after spring deployment.&nbsp;&nbsp; Sirus (sp?) chip may work,&nbsp; but Russian company has a great sleep state DRAM board.&nbsp; From now to March, we should explore both these options.&nbsp; March we make a decision, and then bring in Wayne the help with the implementation.

{color:#ff0000}ACTION{color}:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; ({color:#0000ff}Jim{color})&nbsp;

h3. *Sphere and 4K DWSMS*

•&nbsp;&nbsp; &nbsp;New order of Pucks placed?&nbsp; Charges went through Chris S?
•&nbsp;&nbsp; &nbsp;Serial numbering of pucks
{color:#ff0000}ACTION{color}: Collect and inventory all pucks ({color:#3300ff}Chris S to get Nilo{color}).&nbsp; Then will send 1/2 to Mike Parker to be etched ({color:#0000ff}Scott{color}).&nbsp; Still be to done.
•&nbsp;&nbsp; &nbsp;Pressure pots.&nbsp; Ordered 1 five, 1 ten.

•&nbsp;&nbsp;&nbsp; Battery/power issues for spring deployments
stick with alkaline.&nbsp; Do we need more boxes?&nbsp; Need 4 boxes initially.&nbsp; Not working on low power issues.&nbsp; Must order minimum of 1 box of batteries in early 2008.

We need a total of 6 boxes for the spring deployment, and have 5.&nbsp; 4 of those 5 are D-cells.&nbsp; Two boxes will run around $4K (without batteries)

{color:#ff0000}ACTION{color}: &nbsp; Buy two boxes, populate with D-cells.&nbsp; One with lead-acid will remain lead-acid. ({color:#0000ff}Scott) Jim{color} get account # to charge.

•&nbsp;&nbsp; &nbsp;4K DWSM update
o&nbsp;&nbsp; &nbsp;machining
o&nbsp;&nbsp; &nbsp;proof of concept steel housing?
•&nbsp;&nbsp; &nbsp;Progress on 1K article?

Will not use Ti for the sampling system.&nbsp; Until we prove the aqualung works, no need to make out of Ti.&nbsp; So will make out of SS for around $8K for the housings.&nbsp; Next month we'll build up a plastic system we can run up to 100psi.

{color:#ff0000}ACTION{color}: will try and have model done by end of Jan--depends on pumps ({color:#0000ff}Doug{color})&nbsp;
\\

h3. *Items Pending:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)
Three new surface cans for 2008

{color:#ff0000}ACTION{color}: Get quote from Gene and place order ({color:#0000ff}Jim{color})]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began

*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).
Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays
Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

MELO used was #300034012090780


h4. {color:#ff00cc}ECOHAB--S. California{color}]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
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<property name="spaceKey"><![CDATA[ESPAPP]]></property>
<property name="user"><![CDATA[addie]]></property>
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<property name="user"><![CDATA[jbirch@mbari.org]]></property>
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<property name="name"><![CDATA[favourite]]></property>
<property name="owner"><![CDATA[pami]]></property>
<property name="namespace"><![CDATA[my]]></property>
<property name="creationDate">2008-01-30 11:46:34.003</property>
<property name="lastModificationDate">2008-01-30 12:21:20.213</property>
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<property name="body"><![CDATA[Priority, What we need, (number).&nbsp;

Black \--> we do in house, {color:#0000ff}Blue \--> can be sent out (Mike decides){color}
* 1, Mushroom caps (20)
* 1, Bulkhead V. mounting brackets (6)
* 1, Plate Caps (2)
* 1-Mike, {color:#0000ff}Waste Container (2){color}
* 1-Mike, {color:#0000ff}Waste container supports (6){color}
* 1-Mike, {color:#0000ff}Bag Hanger Assemblies (5){color}

| &nbsp;{color:#009900}Bag Assembly Parts&nbsp;{color} | {color:#009900}For 5 Instruments{color} | {color:#009900}We currently have{color} | {color:#009900}We thus need (minimum){color} |
| Hoops | 10L&nbsp; 5mL&nbsp; 15sm \\ | 4L&nbsp; 1mL&nbsp; 2sm \\ | 6L&nbsp; 4mL&nbsp; 13sm \\ |
| Crescent Closet Bar \\ | 7 | 3 | 4 |
| Bushing Assemb 4/instrument \\ | 20 | 14 | 6 |
* 2, Modem Battery cylinder (1)
* 2, {color:#0000ff}Sample ports (4){color}
* 2, spin can zinc down (3)
* 2, can-side CTD bracket (2)
* 2, {color:#0000ff}sample intake copper screen holder (4){color}
* 2, bail locking plates (4)
* 2, adaptor plate for mooring (2)
* 3, CTV mount (3)
* 3, forearm motor shaft adaptor (2)
* 3, finger motor shaft adaptor (2)
* 3, slot the encoder shafts (8)]]></property>
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<property name="body"><![CDATA[Priority, What we need, (number).&nbsp;

Black \--> we do in house, {color:#0000ff}Blue \--> can be sent out (Mike decides){color}
* 1, Mushroom caps (20) {color:#ff0000}\- Mike has made (5) and will send the rest out for quote (1/31/08){color}
* 1, Bulkhead V. mounting brackets (6)
* -1, Plate Caps (2)- {color:#ff0000}\- (1/31/08){color}
* 1-Mike, {color:#0000ff}Waste Container (2){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08){color}
* 1-Mike, {color:#0000ff}Waste container supports (6){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08){color}
* 1-Mike, {color:#0000ff}Bag Hanger Assemblies (5){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08){color}

| {color:#009900}Bag Assembly Parts&nbsp;{color} | {color:#009900}For 5 Instruments{color} | {color:#009900}We currently have{color} | {color:#009900}We thus need (minimum){color} |
| Hoops | 10L&nbsp; 5mL&nbsp; 15sm \\ | 4L&nbsp; 1mL&nbsp; 2sm \\ | 6L&nbsp; 4mL&nbsp; 13sm \\ |
| Crescent Closet Bar \\ | 7 | 3 | 4 |
| Bushing Assemb 4/instrument \\ | 20 | 14 | 6 |
* 2, Modem Battery cylinder (1)
* 2, {color:#0000ff}Sample ports (4){color}
* 2, spin can zinc down (3)
* 2, can-side CTD bracket (2)
* 2, {color:#0000ff}sample intake copper screen holder (4){color}
* 2, bail locking plates (4)
* 2, adaptor plate for mooring (2)
* 3, CTV mount (3)
* 3, forearm motor shaft adaptor (2)
* 3, finger motor shaft adaptor (2)
* 3, slot the encoder shafts (8)]]></property>
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<property name="body"><![CDATA[Priority, What we need, (number).&nbsp;

Black \--> we do in house, {color:#0000ff}Blue \--> can be sent out (Mike decides){color}
* 1, Mushroom caps (20) {color:#ff0000}\- Mike has made (5) and will send the rest out for quote (1/31/08){color}
* -1, Bulkhead V. mounting brackets (6)- {color:#ff0000}(02/04/08){color}
* -1, Plate Caps (2)- {color:#ff0000}\- (1/31/08){color}
* 1-Mike, {color:#0000ff}Waste Container (2){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08){color}
* 1-Mike, {color:#0000ff}Waste container supports (6){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08){color}
* 1-Mike, {color:#0000ff}Bag Hanger Assemblies (5){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08){color}

| {color:#009900}Bag Assembly Parts&nbsp;{color} | {color:#009900}For 5 Instruments{color} | {color:#009900}We currently have{color} | {color:#009900}We thus need (minimum){color} |
| Hoops | 10L&nbsp; 5mL&nbsp; 15sm \\ | 4L&nbsp; 1mL&nbsp; 2sm \\ | 6L&nbsp; 4mL&nbsp; 13sm \\ |
| Crescent Closet Bar \\ | 7 | 3 | 4 |
| Bushing Assemb 4/instrument \\ | 20 | 14 | 6 |
* 2, Modem Battery cylinder (1)
* 2, {color:#0000ff}Sample ports (4){color}
* 2, spin can zinc down (3)
* 2, can-side CTD bracket (2)
* 2, {color:#0000ff}sample intake copper screen holder (4){color}
* 2, bail locking plates (4)
* 2, adaptor plate for mooring (2)
* -3, CTV mount (3)- {color:#ff0000}(2/04/08){color}
* 3, forearm motor shaft adaptor (2)
* 3, finger motor shaft adaptor (2)
* 3, slot the encoder shafts (8)]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...
]]></property>
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<property name="body"><![CDATA[Priority, What we need, (number).&nbsp;

Black \--> we do in house, {color:#0000ff}Blue \--> can be sent out (Mike decides){color}
* 1, Mushroom caps (20) {color:#ff0000}\- Mike has made (5) and will send the rest out for quote (1/31/08){color}
* -1, Bulkhead V. mounting brackets (6)- {color:#ff0000}(02/04/08){color}
* -1, Plate Caps (2)- {color:#ff0000}\- (1/31/08){color}
* 1-Mike, {color:#0000ff}Waste Container (2){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08){color}
* 1-Mike, {color:#0000ff}Waste container supports (6){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08){color}
* 1-Mike, {color:#0000ff}Bag Hanger Assemblies (5){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08){color}

| {color:#009900}Bag Assembly Parts&nbsp;{color} | {color:#009900}For 5 Instruments{color} | {color:#009900}We currently have{color} | {color:#009900}We thus need (minimum){color} |
| Hoops | 10L&nbsp; 5mL&nbsp; 15sm \\ | 4L&nbsp; 1mL&nbsp; 2sm \\ | 6L&nbsp; 4mL&nbsp; 13sm \\ |
| Crescent Closet Bar \\ | 7 | 3 | 4 |
| Bushing Assemb 4/instrument \\ | 20 | 14 | 6 |
* 2, Modem Battery cylinder (1)
* 2, {color:#0000ff}Sample ports (4){color}
* 2, spin can zinc down (3)
* 2, can-side CTD bracket (2)
* 2, {color:#0000ff}sample intake copper screen holder (4){color}
* 2, bail locking plates (4)
* 2, adaptor plate for mooring (2)
* -3, CTV mount (3)- {color:#ff0000}(2/04/08){color}
* -3, forearm motor shaft adaptor (2)- {color:#ff0000}(02/05/08){color}
* -3, finger motor shaft adaptor (2)- {color:#ff0000}(02/05/08){color}
* 3, slot the encoder shafts (8)]]></property>
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<property name="body"><![CDATA[Priority, What we need, (number).&nbsp;

Black \--> we do in house, {color:#0000ff}Blue \--> can be sent out (Mike decides){color}
* 1, Mushroom caps - 1003526-004 \-(20) {color:#ff0000}\- Mike has made (5) and will send the rest out for quote (1/31/08){color}
* -1, Bulkhead V. mounting brackets (6)- {color:#ff0000}(02/04/08){color}
* -1, Plate Caps (2)- {color:#ff0000}\- (1/31/08){color}
* 1-Mike, {color:#0000ff}Waste Container - 1003526-001 - (2){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08){color}
* 1-Mike, {color:#0000ff}Waste container supports - 1003526-003 - (6){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08){color}
* 1-Mike, {color:#0000ff}Bag Hanger Assemblies - 1003523-01-02-03 - (5){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08){color}

| {color:#009900}Bag Assembly Parts&nbsp;{color} | {color:#009900}For 5 Instruments{color} | {color:#009900}We currently have{color} | {color:#009900}We thus need (minimum){color} |
| Hoops | 10L&nbsp; 5mL&nbsp; 15sm \\ | 4L&nbsp; 1mL&nbsp; 2sm \\ | 6L&nbsp; 4mL&nbsp; 13sm \\ |
| Crescent Closet Bar \\ | 7 | 3 | 4 |
| Bushing Assemb 4/instrument \\ | 20 | 14 | 6 |
* 2, Modem Battery cylinder - 10020051-01 - (1)
* 2, {color:#0000ff}Sample ports - 1002516 - (4){color}
* 2, spin can zinc down (3)
* 2, can-side CTD bracket (2)
* 2, {color:#0000ff}sample intake copper screen holder - 1002516-02 - (4){color}
* 2, bail locking plates (4)
* 2, adaptor plate for mooring (2)
* -3, CTV mount - 1002330-019 - (3)- {color:#ff0000}(2/04/08){color}
* -3, forearm motor shaft adaptor - 1002451-006 - (2)- {color:#ff0000}(02/05/08){color}
* -3, finger motor shaft adaptor - 1002451-006 short - (2)- {color:#ff0000}(02/05/08){color}
* 3, slot the encoder shafts (8)]]></property>
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<property name="body"><![CDATA[Nothing yet. ]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-1.2.jar] to your computer.
# Double-click the jar to run the app.

You can also get the automated image analysis application [here|http://www.mbari.org/staff/brian/software/esp-automated-imaging-0.3.jar]

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|Investigations into Automated Image Analysis].

I'm working on a new method. Documentation is [here|ESP Automated Image Analysis 2]

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter 
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size. 
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | * On Cartridge\\
 No collector/flex lines, limited vol.
* Off Cartridge\\
 Higher Vol, req collector/flex lines | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began

*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).
Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays
Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

h4. {color:#ff00cc}ECOHAB--S. California{color}]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began

*March 5, 2014*

ESP-NEO. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).

Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...]. 

h4. {color:#ff00cc}ECOHAB--S. California{color}]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began

*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).

Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays

Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

h4. {color:#ff00cc}ECOHAB--S. California{color}]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began

*March 5, 2014*

ESP-NEO. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).

Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...]. ]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began

*March 5, 2014*


ESP-NEO. Running WCR and water quality PCR probes
Located at Ocean Pier (extension of Niagara Ave, San Diego).
*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.3.jar] to your computer.
# Double-click the jar to run the app.

You can also get the automated image analysis application [here|http://www.mbari.org/staff/brian/software/esp-automated-imaging-0.3.jar]

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|Investigations into Automated Image Analysis].

I'm working on a new method. Documentation is [here|ESP Automated Image Analysis 2]

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter 
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size. 
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[
h2. ESP Image Analysis Application
There is a standalone user interface for the ESP lab to run automated image analysis at [http://www.mbari.org/staff/brian/pub/esp-autoanalyzer.jar].

h2. Overview of ESP Image Analysis Automation

# [Investigations into Automated Image Analysis]
# [Extracting GAL Point Features]
# [Extracting Image Point Features]
# [Extracting Image Fiducial Features]
# [Point Feature Alignment]

h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 31, 2008*

*11am-12*
Present:
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp; {color:#339999}Hasn't shuffled pucks yet.&nbsp; Almost finished testing{color}
* Update on valve cold-testing of MACK.&nbsp; {color:#339999}Still to begin{color}
* Jan 15-29 both Bruce & Neo to be re-valved.&nbsp; Progress? {color:#ff0000}Not begun{color} yet
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; {color:#339999}Not ready until cold-testing finished{color}
* New syringe cost.&nbsp; Acct to charge?&nbsp;&nbsp; {color:#339999}50 syringes&nbsp; \~$10K charge to 900612.&nbsp; May start to identify people that want these new syringes (Chris S.){color}
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp; {color:#339999}Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612 (look to see if he has time (Jim)&nbsp; maybe a subaccount (.99 for CIP)).{color}
* Mock deployment schedule and Spring field trials
* PROCUREMENT AND BUILD SCHEDULE FOR NEXT 2 CORES (WHOI & CMORE)\\

ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp; {color:#0000ff}Finished{color}\\

+Action Items+

ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp; {color:#0000ff}Finished{color}

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#0000ff}Finished{color}

h3.


h3. MFB

Discussion Items:

ACTION: Will work on figuring cable problem to three-way valves. (Addie) {color:#0000ff}Finished{color}
ACTION: Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie) {color:#0000ff}Finished{color}
ACTION: Fan not working on PCR module and Addie will try and track down why (check in various terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie); {color:#0000ff}Finished{color}

h3. Software

* Gain/offset for heating cycles installed?&nbsp; Still trying to test
* Has 'Cheat Sheet' for new sample collection parameters been distributed? (Not done)
* Firmware updated on Mack, Bruck & Neo? still testing

+Action Items:+&nbsp;
ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent): implemented but figuring when it should happen.&nbsp;
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)
ACTION:&nbsp; Update firmware on Mack, Bruce, Neo with the 'slightly modified version, and email the changes within this new firmware to everyone (Brent) DONE

Brent will work on operational model for temp control.&nbsp; Get it ready for Sept that will be implemented with the MFB. (Brent)&nbsp;

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}



h3. Sphere and 4K DWSMS

* Oil cold testing.&nbsp; Finished?&nbsp; {color:#339999}100 cst goes 150 cst when in cold.&nbsp; It's a significant increase but can be counterd by buying lower viscosity oil.{color}
* &nbsp;
* Screen drawings.&nbsp; Checked?&nbsp; Ready for order?&nbsp; Photofab drawings have been looked at and they have a new spec to send to PFI.&nbsp; The way they fabbed last time they took out too much b/w holes.&nbsp; Doug wants them etched to a certain mass.&nbsp;

ACTION:&nbsp; Scott to send samples and current idea to see if they can do it to weight. (Scott will mail samples to them)&nbsp; Chris and Roman have spec for scintered frits and are discussing how many to order.&nbsp; They have a quote.
* Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}
* DWSM progress?&nbsp;&nbsp; {color:#339999}Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.{color}

No word on sphere.&nbsp; Discussion about Tapemation machining and how we should get insurance or discuss protection.&nbsp;

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim)

{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
&nbsp;

h3. GUI Development

* Mission script progress

ACTION:&nbsp; Will try and have mission script GUI out next week.&nbsp; Kevin will meet with Chris S. (Kevin)
* Adjustment of project #'s in JIRA

ACTION: Kevin will delete one account and the one to use is ESP Gen II. {color:#0000ff}FINISHED{color}\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[# [2008 Q1-Q2 Schedule (rev 1)]
# [Machinist build schedule (Feb 2007)]]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 31, 2008*

*11am-12*
Present:
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp;&nbsp;
** {color:#339999}Mack has been cold-tested and Brent is working on temp sensor testing.{color}
** {color:#339999}Bruce--all valves are in, hand mostly assembled, still to finish plumbing{color}
* Mike Parker Machining [list|ESPAPP:Machinist build schedule (Feb 2007)] \-\- working quickly through it
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; {color:#339999}N{color}
** {color:#339999}New hands to be ordered this summer.&nbsp; XX hand assemblies + 3 sets of fingers with new fulcrum positions to replace the existing 'new' fingers{color}
* New syringe cost.&nbsp;
** {color:#339999}Still not heard back from company{color}
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp;
** {color:#339999}Jose still forming the database.&nbsp; Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612,&nbsp; maybe a subaccount (.99 for CIP)).{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp; {color:#0000ff}Finished{color}
ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp; {color:#0000ff}Finished{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#0000ff}Finished{color}

h3.


h3. MFB

Discussion Items:
* Getting excellent yields out of solid-phase-extraction--Good job Addie and Chris P\!\!
* Mixing column basically finished
* next week will make extract from seawater lysate and compare to bench-top
* in parallel, do dye tests with heater block.

ACTION:&nbsp; Hook up heater block and test diodes for fluorescence sensitivity. (Addie)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will work on figuring cable problem to three-way valves. (Addie) {color:#0000ff}Finished{color}
ACTION: Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie) {color:#0000ff}Finished{color}
ACTION: Fan not working on PCR module and Addie will try and track down why (check in various terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie); {color:#0000ff}Finished{color}

h3. Software

* puck heating control
** now can send a temperature to puck and it gets there in 2-3 minutes with little overshoot
* Brent would like to pull calibration values out into a structure, since they are different on each instrument

+Action Items:+&nbsp;

ACTION:&nbsp; Finish by Feb 6 the temperature calibration model, incorporating Scott's prior work if possible. (Brent)
ACTION:&nbsp; make another temperature puck (Scott)
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment (Brent): {color:#ff0000}Low priority Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}

h3. Sphere and 4K DWSMS

* Screen drawings.&nbsp;

Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}
* DWSM progress?&nbsp;&nbsp; {color:#339999}Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.{color}

{color:#000000}ACTION:{color}&nbsp; Waiting for company to return yes/no on whether they can manufacture screens to mass instead of size. (Doug/Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim): {color:#0000ff}Finished{color} (Tapemation is it unless we want to go back east)&nbsp;

h3. GUI Development

* Mission script GUI introduction

Kevin showed how to use the mission script GUI located [here|http://predator.shore.mbari.org/esp_gui/launch.jnlp].

Bugs for this GUI can be reported [here|http://oceana.shore.mbari.org:8082].&nbsp;

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 31, 2008*

*11am-12*
Present:
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp;&nbsp;
** {color:#339999}Mack has been cold-tested and Brent is working on temp sensor testing.{color}
** {color:#339999}Bruce--all valves are in, hand mostly assembled, still to finish plumbing{color}
* Mike Parker Machining [list|ESPAPP:Machinist build schedule (Feb 2007)] \-\- working quickly through it
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; {color:#339999}N{color}
** {color:#339999}New hands to be ordered this summer.&nbsp; XX hand assemblies + 3 sets of fingers with new fulcrum positions to replace the existing 'new' fingers{color}
* New syringe cost.&nbsp;
** {color:#339999}Still not heard back from company{color}
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp;
** {color:#339999}Jose still forming the database.&nbsp; Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612,&nbsp; maybe a subaccount (.99 for CIP)).{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp; {color:#0000ff}Finished{color}
ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp; {color:#0000ff}Finished{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#0000ff}Finished{color}

h3. MFB

Discussion Items:
* Getting excellent yields out of solid-phase-extraction--Good job Addie and Chris P\!\!
* Mixing column basically finished
* next week will make extract from seawater lysate and compare to bench-top
* in parallel, do dye tests with heater block.

ACTION:&nbsp; Hook up heater block and test diodes for fluorescence sensitivity. (Addie)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will work on figuring cable problem to three-way valves. (Addie) {color:#0000ff}Finished{color}
ACTION: Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie) {color:#0000ff}Finished{color}
ACTION: Fan not working on PCR module and Addie will try and track down why (check in various terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie); {color:#0000ff}Finished{color}

h3. Software

* puck heating control
** now can send a temperature to puck and it gets there in 2-3 minutes with little overshoot
* Brent would like to pull calibration values out into a structure, since they are different on each instrument

+Action Items:+&nbsp;

ACTION:&nbsp; Finish by Feb 6 the temperature calibration model, incorporating Scott's prior work if possible. (Brent)
ACTION:&nbsp; make another temperature puck (Scott)
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment (Brent): {color:#ff0000}Low priority Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}

h3. Sphere and 4K DWSMS

* Screen drawings.&nbsp;

Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}
* DWSM progress?&nbsp;&nbsp; {color:#339999}Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.{color}

{color:#000000}ACTION:{color}&nbsp; Waiting for company to return yes/no on whether they can manufacture screens to mass instead of size. (Doug/Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim): {color:#0000ff}Finished{color} (Tapemation is it unless we want to go back east)&nbsp;

h3. &nbsp;


h3. GUI Development

* Mission script GUI introduction

Kevin showed how to use the mission script GUI located [here|http://predator.shore.mbari.org/esp_gui/launch.jnlp].
Bugs for this GUI can be reported [here|http://oceana.shore.mbari.org:8082].&nbsp;\\ \\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 31, 2008*

*11am-12*
Present:
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp;&nbsp;
** {color:#339999}Mack has been cold-tested and Brent is working on temp sensor testing.{color}
** {color:#339999}Bruce--all valves are in, hand mostly assembled, still to finish plumbing{color}
* Mike Parker Machining [list|ESPAPP:Machinist build schedule (Feb 2007)] \-\- working quickly through it
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; {color:#339999}N{color}
** {color:#339999}New hands to be ordered this summer.&nbsp; XX hand assemblies + 3 sets of fingers with new fulcrum positions to replace the existing 'new' fingers{color}
* New syringe cost.&nbsp;
** {color:#339999}Still not heard back from company{color}
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp;
** {color:#339999}Jose still forming the database.&nbsp; Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612,&nbsp; maybe a subaccount (.99 for CIP)).{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp; {color:#0000ff}Finished{color}
ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp; {color:#0000ff}Finished{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#0000ff}Finished{color}

h3.


h3. MFB

Discussion Items:
* Getting excellent yields out of solid-phase-extraction--Good job Addie and Chris P\!\!
* Mixing column basically finished
* next week will make extract from seawater lysate and compare to bench-top
* in parallel, do dye tests with heater block.

ACTION:&nbsp; Hook up heater block and test diodes for fluorescence sensitivity. (Addie)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will work on figuring cable problem to three-way valves. (Addie) {color:#0000ff}Finished{color}
ACTION: Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie) {color:#0000ff}Finished{color}
ACTION: Fan not working on PCR module and Addie will try and track down why (check in various terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie); {color:#0000ff}Finished{color}

h3. Software

* puck heating control
** now can send a temperature to puck and it gets there in 2-3 minutes with little overshoot
* Brent would like to pull calibration values out into a structure, since they are different on each instrument

+Action Items:+&nbsp;

ACTION:&nbsp; Finish by Feb 6 the temperature calibration model, incorporating Scott's prior work if possible. (Brent)
ACTION:&nbsp; make another temperature puck (Scott)
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment (Brent): {color:#ff0000}Low priority Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}

h3. Sphere and 4K DWSMS

* Screen drawings.&nbsp;

Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}
* DWSM progress?&nbsp;&nbsp; {color:#339999}Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.{color}

{color:#000000}ACTION:{color}&nbsp; Waiting for company to return yes/no on whether they can manufacture screens to mass instead of size. (Doug/Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim): {color:#0000ff}Finished{color} (Tapemation is it unless we want to go back east)&nbsp;

h3. GUI Development

* Mission script GUI introduction

Kevin showed how to use the mission script GUI located [here|GUI Web Start|http://predator.shore.mbari.org/esp_gui/launch.jnlp].
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 31, 2008*

*11am-12*
Present:
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp;&nbsp;
** {color:#339999}Mack has been cold-tested and Brent is working on temp sensor testing.{color}
** {color:#339999}Bruce--all valves are in, hand mostly assembled, still to finish plumbing{color}
* Mike Parker Machining [list|ESPAPP:Machinist build schedule (Feb 2007)] \-\- working quickly through it
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; {color:#339999}N{color}
** {color:#339999}New hands to be ordered this summer.&nbsp; XX hand assemblies + 3 sets of fingers with new fulcrum positions to replace the existing 'new' fingers{color}
* New syringe cost.&nbsp;
** {color:#339999}Still not heard back from company{color}
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp;
** {color:#339999}Jose still forming the database.&nbsp; Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612,&nbsp; maybe a subaccount (.99 for CIP)).{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp; {color:#0000ff}Finished{color}
ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp; {color:#0000ff}Finished{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#0000ff}Finished{color}

h3.


h3. MFB

Discussion Items:
* Getting excellent yields out of solid-phase-extraction--Good job Addie and Chris P\!\!
* Mixing column basically finished
* next week will make extract from seawater lysate and compare to bench-top
* in parallel, do dye tests with heater block.

ACTION:&nbsp; Hook up heater block and test diodes for fluorescence sensitivity. (Addie)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will work on figuring cable problem to three-way valves. (Addie) {color:#0000ff}Finished{color}
ACTION: Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie) {color:#0000ff}Finished{color}
ACTION: Fan not working on PCR module and Addie will try and track down why (check in various terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie); {color:#0000ff}Finished{color}

h3. Software

* puck heating control
** now can send a temperature to puck and it gets there in 2-3 minutes with little overshoot
* Brent would like to pull calibration values out into a structure, since they are different on each instrument

+Action Items:+&nbsp;

ACTION:&nbsp; Finish by Feb 6 the temperature calibration model, incorporating Scott's prior work if possible. (Brent)
ACTION:&nbsp; make another temperature puck (Scott)
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment (Brent): {color:#ff0000}Low priority Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}

h3. Sphere and 4K DWSMS

* Screen drawings.&nbsp;

Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}
* DWSM progress?&nbsp;&nbsp; {color:#339999}Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.{color}

{color:#000000}ACTION:{color}&nbsp; Waiting for company to return yes/no on whether they can manufacture screens to mass instead of size. (Doug/Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim): {color:#0000ff}Finished{color} (Tapemation is it unless we want to go back east)&nbsp;

h3. GUI Development

* Mission script GUI introduction

Kevin showed how to use the mission script GUI located [here|http://predator.shore.mbari.org/esp_gui/launch.jnlp].
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 31, 2008*

*11am-12*
Present:
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp;&nbsp;
** {color:#339999}Mack has been cold-tested and Brent is working on temp sensor testing.{color}
** {color:#339999}Bruce--all valves are in, hand mostly assembled, still to finish plumbing{color}
* Mike Parker Machining [list|ESPAPP:Machinist build schedule (Feb 2007)] \-\- working quickly through it
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; {color:#339999}N{color}
** {color:#339999}New hands to be ordered this summer.&nbsp; XX hand assemblies + 3 sets of fingers with new fulcrum positions to replace the existing 'new' fingers{color}
* New syringe cost.&nbsp;
** {color:#339999}Still not heard back from company{color}
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp;
** {color:#339999}Jose still forming the database.&nbsp; Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612 (look to see if he has time (Jim)&nbsp; maybe a subaccount (.99 for CIP)).{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}\\

&nbsp;ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp; {color:#0000ff}Finished{color}
&nbsp;ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp; {color:#0000ff}Finished{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#0000ff}Finished{color}

h3.


h3. MFB

Discussion Items:

ACTION: Will work on figuring cable problem to three-way valves. (Addie) {color:#0000ff}Finished{color}
ACTION: Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie) {color:#0000ff}Finished{color}
ACTION: Fan not working on PCR module and Addie will try and track down why (check in various terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie); {color:#0000ff}Finished{color}

h3. Software

* Gain/offset for heating cycles installed?&nbsp; Still trying to test
* Has 'Cheat Sheet' for new sample collection parameters been distributed? (Not done)
* Firmware updated on Mack, Bruck & Neo? still testing

+Action Items:+&nbsp;
ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent):
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)

Brent will work on operational model for temp control.&nbsp; Get it ready for Sept that will be implemented with the MFB. (Brent)&nbsp;

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment (Brent): {color:#ff0000}Low priority Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}

h3. Sphere and 4K DWSMS

* Screen drawings.&nbsp; Checked?&nbsp; Ready for order?&nbsp; Photofab drawings have been looked at and they have a new spec to send to PFI.&nbsp; The way they fabbed last time they took out too much b/w holes.&nbsp; Doug wants them etched to a certain mass.&nbsp;

ACTION:&nbsp; Scott to send samples and current idea to see if they can do it to weight. (Scott will mail samples to them)&nbsp; Chris and Roman have spec for scintered frits and are discussing how many to order.&nbsp; They have a quote.
* Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}
* DWSM progress?&nbsp;&nbsp; {color:#339999}Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.{color}

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim)

{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
&nbsp;

h3. GUI Development

* Mission script GUI introduction

\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 31, 2008*

*11am-12*
Present:
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp; {color:#339999}Hasn't shuffled pucks yet.&nbsp; Almost finished testing{color}
* Update on valve cold-testing of MACK.&nbsp; {color:#339999}Still to begin{color}
* Both Bruce & Neo to be re-valved.&nbsp; Progress?&nbsp;
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; {color:#339999}Not ready until cold-testing finished{color}
* New syringe cost.&nbsp; Acct to charge?&nbsp;&nbsp; {color:#339999}50 syringes&nbsp; \~$10K charge to 900612.&nbsp; May start to identify people that want these new syringes (Chris S.){color}
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp; {color:#339999}Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612 (look to see if he has time (Jim)&nbsp; maybe a subaccount (.99 for CIP)).{color}

+Action Items+\\ \\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}\\

&nbsp;ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp; {color:#0000ff}Finished{color}
&nbsp;ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp; {color:#0000ff}Finished{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#0000ff}Finished{color}

h3.


h3. MFB

Discussion Items:

ACTION: Will work on figuring cable problem to three-way valves. (Addie) {color:#0000ff}Finished{color}
ACTION: Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie) {color:#0000ff}Finished{color}
ACTION: Fan not working on PCR module and Addie will try and track down why (check in various terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie); {color:#0000ff}Finished{color}

h3. Software

* Gain/offset for heating cycles installed?&nbsp; Still trying to test
* Has 'Cheat Sheet' for new sample collection parameters been distributed? (Not done)
* Firmware updated on Mack, Bruck & Neo? still testing

+Action Items:+&nbsp;
ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent):
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)

Brent will work on operational model for temp control.&nbsp; Get it ready for Sept that will be implemented with the MFB. (Brent)&nbsp;

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment (Brent): {color:#ff0000}Low priority Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}

h3. Sphere and 4K DWSMS

* Screen drawings.&nbsp; Checked?&nbsp; Ready for order?&nbsp; Photofab drawings have been looked at and they have a new spec to send to PFI.&nbsp; The way they fabbed last time they took out too much b/w holes.&nbsp; Doug wants them etched to a certain mass.&nbsp;

ACTION:&nbsp; Scott to send samples and current idea to see if they can do it to weight. (Scott will mail samples to them)&nbsp; Chris and Roman have spec for scintered frits and are discussing how many to order.&nbsp; They have a quote.
* Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}
* DWSM progress?&nbsp;&nbsp; {color:#339999}Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.{color}

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim)

{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
&nbsp;

h3. GUI Development

* Mission script GUI introduction

\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 31, 2008*

*11am-12*
Present:
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp;&nbsp;
** {color:#339999}Mack has been cold-tested and Brent is working on temp sensor testing.{color}
** {color:#339999}Bruce--all valves are in, hand mostly assembled, still to finish plumbing{color}
* Mike Parker Machining [list|ESPAPP:Machinist build schedule (Feb 2007)] \-\- working quickly through it
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; {color:#339999}N{color}
** {color:#339999}New hands to be ordered this summer.&nbsp; XX hand assemblies + 3 sets of fingers with new fulcrum positions to replace the existing 'new' fingers{color}
* New syringe cost.&nbsp;
** {color:#339999}Still not heard back from company{color}
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp;
** {color:#339999}Jose still forming the database.&nbsp; Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612,&nbsp; maybe a subaccount (.99 for CIP)).{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}\\

&nbsp;ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp; {color:#0000ff}Finished{color}
&nbsp;ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp; {color:#0000ff}Finished{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#0000ff}Finished{color}

h3.


h3. MFB

Discussion Items:

ACTION: Will work on figuring cable problem to three-way valves. (Addie) {color:#0000ff}Finished{color}
ACTION: Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie) {color:#0000ff}Finished{color}
ACTION: Fan not working on PCR module and Addie will try and track down why (check in various terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie); {color:#0000ff}Finished{color}

h3. Software

* Gain/offset for heating cycles installed?&nbsp; Still trying to test
* Has 'Cheat Sheet' for new sample collection parameters been distributed? (Not done)
* Firmware updated on Mack, Bruck & Neo? still testing

+Action Items:+&nbsp;
ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent):
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)

Brent will work on operational model for temp control.&nbsp; Get it ready for Sept that will be implemented with the MFB. (Brent)&nbsp;

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment (Brent): {color:#ff0000}Low priority Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}

h3. Sphere and 4K DWSMS

* Screen drawings.&nbsp; Checked?&nbsp; Ready for order?&nbsp; Photofab drawings have been looked at and they have a new spec to send to PFI.&nbsp; The way they fabbed last time they took out too much b/w holes.&nbsp; Doug wants them etched to a certain mass.&nbsp;

ACTION:&nbsp; Scott to send samples and current idea to see if they can do it to weight. (Scott will mail samples to them)&nbsp; Chris and Roman have spec for scintered frits and are discussing how many to order.&nbsp; They have a quote.
* Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}
* DWSM progress?&nbsp;&nbsp; {color:#339999}Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.{color}

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim)

{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
&nbsp;

h3. GUI Development

* Mission script GUI introduction

\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 24, 2008*

*11am-12*
Present: Jim, Doug, Scott, Addie, Kevin, Brent, Chris S.
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp; Hasn't shuffled pucks yet.&nbsp; Almost finished testing
* Update on valve cold-testing of MACK.&nbsp; Still to begin
* Jan 15-29 both Bruce & Neo to be re-valved.&nbsp; Progress? {color:#ff0000}Not begun{color} yet
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; Not ready until cold-testing finished
* New syringe cost.&nbsp; Acct to charge?&nbsp;&nbsp; 50 syringes&nbsp; \~$10K charge to 900612.&nbsp; May start to identify people that want these new syringes (Chris S.)
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp; Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612 (look to see if he has time (Jim)&nbsp; maybe a subaccount (.99 for CIP)).
* Mock deployment schedule and Spring field trials
* PROCUREMENT AND BUILD SCHEDULE FOR NEXT 2 CORES (WHOI & CMORE)

&nbsp;*Two Options for build of two more cores:*

Buy parts under another grant and then transfer charges to WHOI grant when money comes in in August 2008.&nbsp; This is dangerous as WHOI may not get money and if we've bought ahead, we'd be stuck with parts, and have hit another grant very hard.
CMORE machine will initially be stationed here at MBARI but eventually goes to CMORE partner.&nbsp; The best plan is to use BRUCE/MACK as the WHOI & CMORE machines, and have parts for their replacements on hand. &nbsp;&nbsp;

Chris thinks--do we know what we need to order.&nbsp; Get all ready to cut and look to mid-summer for procurement and build starting in Sept.&nbsp; By that time more money comes through and we could add to the purchases.&nbsp; This applies to all Jose's boards except the MFB boards.&nbsp; Now we should order enough dwarfs for MFB and spares. For MFB boards split between 701312 and 800560.&nbsp; Make sure subaccount charges are correct.&nbsp; The summer order would be the rest and the long-lead orders.&nbsp;
\\

Second MFB is parted and here.&nbsp; Chris and Jim will work with grants to make sure money is spent correctly (reallocate MOORE monies).


Neo has been capitalized so buying any more parts goes to a different account (maintenance or equipment supplies, not the NEO CIP account).&nbsp;

[Q1-Q2 2008|ESPAPP:2008 Q1-Q2 Schedule] schedule has slipped.&nbsp; Must shift our schedule back one month.&nbsp; Maybe can shave mock-deployment by running harder/faster.&nbsp;

ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp;
\\

+Action Items+

ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp; {color:#ff0000}In progress:{color}

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}

h3.


h3. MFB

Discussion Items:
* Motor control cables lengthened?&nbsp; {color:#0000ff}Finished{color}

problem in cable that goes to 3-way valve.&nbsp; Jose can't figure it out.&nbsp;

ACTION: Will work on figuring cable problem. (Addie)
* Heater block re-plumbed?&nbsp; Owner's manual written detailing new drivers?
* Begin PCR tests?.

LLNL commands are now in Ruby (via Bob Herlien) and Addie has placed on Confluence a '[users manual|ESPAPP:Micro-Fluidics Block^~$B PCR Module Users Manual V1.0.doc]' for the PCR module.&nbsp; Software works well and easy to write scripts.

Fan not working on PCR module and Addie will try and track down why (check in various terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie)

ACTION: write Tony at LLNL for advice. {color:#0000ff}FINISHED{color}&nbsp;

Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie)&nbsp;

h3. Software

* Gain/offset for heating cycles installed?&nbsp; Still trying to test
* Has 'Cheat Sheet' for new sample collection parameters been distributed? (Not done)
* Firmware updated on Mack, Bruck & Neo? still testing

+Action Items:+&nbsp;
ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent): implemented but figuring when it should happen.&nbsp;
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)
ACTION:&nbsp; Update firmware on Mack, Bruce, Neo with the 'slightly modified version, and email the changes within this new firmware to everyone (Brent) DONE

Brent will work on operational model for temp control.&nbsp; Get it ready for Sept that will be implemented with the MFB. (Brent)&nbsp;

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress{color}

h3. Sphere and 4K DWSMS

* Oil cold testing.&nbsp; Finished?&nbsp; 100 cst goes 150 cst when in cold.&nbsp; It's a significant but buy new lower viscosity.
* &nbsp;
* Screen drawings.&nbsp; Checked?&nbsp; Ready for order?&nbsp; Photofab drawings have been looked at and they have a new spec they are sending to PFI.&nbsp; The way they fabbed last time they took out too much b/w holes.&nbsp; Doug wants them etched to a certain mass.&nbsp; Scott to send samples and current idea to see if they can do it to weight. (Scott will mail samples to them)&nbsp; Chris and Roman have spec for scintered frits and are discussing how many to order.&nbsp; They have a quote.
* &nbsp;
* Battery boxes?&nbsp; Scott still waiting to hear.
* DWSM progress?&nbsp;&nbsp; Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.

No word on sphere.&nbsp; Discussion about Tapemation machining and how we should get insurance or discuss protection.&nbsp;

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim)

{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
&nbsp;

h3. GUI Development

* Mission script progress

ACTION:&nbsp; Will try and have mission script GUI out next week.&nbsp; Kevin will meet with Chris S. (Kevin)

* Adjustment of project #'s in JIRA

ACTION: Kevin will delete one account and the one to use is ESP Gen II. {color:#0000ff}FINISHED{color}\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[# [2008 Q1-Q2 Schedule]]]></property>
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<property name="body"><![CDATA[h1. Project Pages

# Design
# Meetings
#]]></property>
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<property name="body"><![CDATA[This is the home page for the 900612 2G ESP Applications space.]]></property>
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<property name="body"><![CDATA[Priority, What we need, (number).&nbsp;

Black \--> we do in house, {color:#0000ff}Blue \--> can be sent out (Mike decides){color}

* 1, Mushroom caps (20)
* 1, Bulkhead V. mounting brackets (6)
* 1, Plate Caps (2)
* 1-Mike, {color:#0000ff}Waste Container (2){color}
* 1-Mike, {color:#0000ff}Waste container supports (6){color}
* 1-Mike, {color:#0000ff}Bag Hanger Assemblies (5){color}
* 2, Modem Battery cylinder (1)
* 2, {color:#0000ff}Sample ports (4){color}
* 2, spin can zinc down (3)
* 2, can-side CTD bracket (2)
* 2, {color:#0000ff}sample intake copper screen holder (4){color}
* 2, bail locking plates (4)
* 2, adaptor plate for mooring (2)
* 3, CTV mount (3)
* 3, forearm motor shaft adaptor (2)
* 3, finger motor shaft adaptor (2)
* 3, slot the encoder shafts (8)]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]]]></property>
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<property name="body"><![CDATA[Priority, What we need, (number).&nbsp;

Black \--> we do in house, {color:#0000ff}Blue \--> can be sent out (Mike decides){color}
* 1, Mushroom caps (20)
* 1, Bulkhead V. mounting brackets (6)
* 1, Plate Caps (2)
* 1-Mike, {color:#0000ff}Waste Container (2){color}
* 1-Mike, {color:#0000ff}Waste container supports (6){color}
* 1-Mike, {color:#0000ff}Bag Hanger Assemblies (5){color}| {color:#009900}Bag Assembly Parts&nbsp;{color} | {color:#009900}For 5 Instruments&nbsp;{color} | {color:#009900}&nbsp;We currently have{color}\\ | {color:#009900}We thus need (minimum)&nbsp;{color} |
| Hoops | 10L&nbsp; 5mL&nbsp; 15sm\\ | 4L&nbsp; 1mL&nbsp; 2sm\\ | 6L&nbsp; 4mL&nbsp; 13sm\\ |
| Crescent Closet Bar\\ | 7 | 3 | 4 |
| Bushing Assemb 4/instrument\\ | 20 | 14 | 6 |
* 2, Modem Battery cylinder (1)
* 2, {color:#0000ff}Sample ports (4){color}
* 2, spin can zinc down (3)
* 2, can-side CTD bracket (2)
* 2, {color:#0000ff}sample intake copper screen holder (4){color}
* 2, bail locking plates (4)
* 2, adaptor plate for mooring (2)
* 3, CTV mount (3)
* 3, forearm motor shaft adaptor (2)
* 3, finger motor shaft adaptor (2)
* 3, slot the encoder shafts (8)]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies / Development needs\\ | Manufacturers/\\
 Collaborators\\ | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ | 4 |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer\\
 RLT, RLT+, >RNA & DNA
* SPR buffer\\
 Aq Methanol | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | * Microsonic\\
 w/ w.o beads
* Magnet flipper
* Bead Mill
* Grinder | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | * Qiagen Membrane
* iFast
* Custom silica column
*  | 4 |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 31, 2008*

*11am-12*
Present:
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp; {color:#339999}Hasn't shuffled pucks yet.&nbsp; Almost finished testing{color}
* Update on valve cold-testing of MACK.&nbsp; {color:#339999}Still to begin{color}
* Jan 15-29 both Bruce & Neo to be re-valved.&nbsp; Progress? {color:#ff0000}Not begun{color} yet
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; {color:#339999}Not ready until cold-testing finished{color}
* New syringe cost.&nbsp; Acct to charge?&nbsp;&nbsp; {color:#339999}50 syringes&nbsp; \~$10K charge to 900612.&nbsp; May start to identify people that want these new syringes (Chris S.){color}
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp; {color:#339999}Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612 (look to see if he has time (Jim)&nbsp; maybe a subaccount (.99 for CIP)).{color}
* Mock deployment schedule and Spring field trials
* PROCUREMENT AND BUILD SCHEDULE FOR NEXT 2 CORES (WHOI & CMORE)

&nbsp;*Two Options for build of two more cores:*

Buy parts under another grant and then transfer charges to WHOI grant when money comes in in August 2008.&nbsp; This is dangerous as WHOI may not get money and if we've bought ahead, we'd be stuck with parts, and have hit another grant very hard.
CMORE machine will initially be stationed here at MBARI but eventually goes to CMORE partner.&nbsp; The best plan is to use BRUCE/MACK as the WHOI & CMORE machines, and have parts for their replacements on hand. &nbsp;&nbsp;

Chris thinks--do we know what we need to order.&nbsp; Get all ready to cut and look to mid-summer for procurement and build starting in Sept.&nbsp; By that time more money comes through and we could add to the purchases.&nbsp; This applies to all Jose's boards except the MFB boards.&nbsp; Now we should order enough dwarfs for MFB and spares. For MFB boards split between 701312 and 800560.&nbsp; Make sure subaccount charges are correct.&nbsp; The summer order would be the rest and the long-lead orders.&nbsp;
\\

Second MFB is parted and here.&nbsp; Chris and Jim will work with grants to make sure money is spent correctly (reallocate MOORE monies).

Neo has been capitalized so buying any more parts goes to a different account (maintenance or equipment supplies, not the NEO CIP account).&nbsp;

Q1-Q2 2008 schedule has slipped.&nbsp; Must shift our schedule back one month.&nbsp; Maybe can shave mock-deployment by running harder/faster.&nbsp;

ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp;
\\

+Action Items+

ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp; {color:#0000ff}Finished{color}

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#0000ff}Finished{color}

h3.


h3. MFB

Discussion Items:

ACTION: Will work on figuring cable problem to three-way valves. (Addie)
ACTION: Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie)&nbsp;

h3.

* Heater block re-plumbed?&nbsp; Owner's manual written detailing new drivers?
* Begin PCR tests?.

LLNL commands are now in Ruby (via Bob Herlien) and Addie has placed on Confluence a 'users manual' for the PCR module.&nbsp; Software works well and easy to write scripts.

Fan not working on PCR module and Addie will try and track down why (check in various terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie); {color:#0000ff}Finished{color}


ACTION: write Tony at LLNL for advice. {color:#0000ff}FINISHED{color}&nbsp;

h3. Software

* Gain/offset for heating cycles installed?&nbsp; Still trying to test
* Has 'Cheat Sheet' for new sample collection parameters been distributed? (Not done)
* Firmware updated on Mack, Bruck & Neo? still testing

+Action Items:+&nbsp;
ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent): implemented but figuring when it should happen.&nbsp;
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)
ACTION:&nbsp; Update firmware on Mack, Bruce, Neo with the 'slightly modified version, and email the changes within this new firmware to everyone (Brent) DONE

Brent will work on operational model for temp control.&nbsp; Get it ready for Sept that will be implemented with the MFB. (Brent)&nbsp;

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress{color}

h3. Sphere and 4K DWSMS

* Oil cold testing.&nbsp; Finished?&nbsp; {color:#339999}100 cst goes 150 cst when in cold.&nbsp; It's a significant increase but can be counterd by buying lower viscosity oil.{color}
* &nbsp;
* Screen drawings.&nbsp; Checked?&nbsp; Ready for order?&nbsp; Photofab drawings have been looked at and they have a new spec to send to PFI.&nbsp; The way they fabbed last time they took out too much b/w holes.&nbsp; Doug wants them etched to a certain mass.&nbsp;

ACTION:&nbsp; Scott to send samples and current idea to see if they can do it to weight. (Scott will mail samples to them)&nbsp; Chris and Roman have spec for scintered frits and are discussing how many to order.&nbsp; They have a quote.
* Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}
* DWSM progress?&nbsp;&nbsp; {color:#339999}Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.{color}

No word on sphere.&nbsp; Discussion about Tapemation machining and how we should get insurance or discuss protection.&nbsp;

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim)

{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
&nbsp;

h3. GUI Development

* Mission script progress

ACTION:&nbsp; Will try and have mission script GUI out next week.&nbsp; Kevin will meet with Chris S. (Kevin)
* Adjustment of project #'s in JIRA

ACTION: Kevin will delete one account and the one to use is ESP Gen II. {color:#0000ff}FINISHED{color}\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 17, 2008*

*11am-12*
Present: Jim, Doug, Addie, Scott, Cheri, Brent, Kevin

h3. Tech Transfer


h6. Discussion Items:

* Arm status update
* Environmental test chamber update

*Arm/Hand*.&nbsp; Removed Bruce from cold testing, and _almost_ finished with hand cold testing.&nbsp; Removed hand from Bruce and installed on Mack. Plan is to finish cold-test on hand and cold-test valves simultaneously on Mack.&nbsp; First priority in cold is to finish testing hand gripper.&nbsp; Once it passes, Mike will get green-light parts of the other hands (first 3 old action items).&nbsp; Order is placed with Maxxon for new forearm motors (maybe 6-8 weeks).&nbsp; Small order of fluidic fittings still needed for all of them.&nbsp; (Cheri)

*ETC* (Environmental Test Chamber).&nbsp; Cold box finished, electrical connectors in, fluidic connectors still need to be put in.&nbsp; New rotary valves all on Mack and being homed and calibrated.&nbsp; All we be ready for cold testing by end of day.

+Action Items+

ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp;

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}
{color:#000000}ACTION:{color}&nbsp; cannot purchase on 708 grant yet.&nbsp; 701312.04 should take all cost.&nbsp; Change:&nbsp; Order only 2 cans (Jim):&nbsp; {color:#0000ff}DONE; ordered 1-11-08{color}
ACTION:&nbsp; talk to Jose to figure a solution to broken home sensor cable. (Scott/Doug/Cheri){color:}&nbsp;{color} {color:#0000ff}DONE{color}
{color:}ACTION:&nbsp; Contact MAXON about forearm motors (Cheri){color} {color:#0000ff}DONE: ordered 1-14-08{color}
{color:#000000}ACTION:{color}&nbsp; confirm we have 3 swapable EM cables&nbsp; (Jim) {color:#0000ff}DONE: confer w/group and decide 1 spare is enough{color}

h3.


h3. MFB

Discussion Items:

•&nbsp;&nbsp;&nbsp; Syringe positioning

Syringe now oriented like other syringes on the core, i.e., pointing 'downward', and working well.&nbsp; Still waiting to test as several cables needed to be lengthened.

•&nbsp;&nbsp;&nbsp; Status of mixing column for extraction lysate.

Unable to build a 10cm mixing column because the use of 2 reducing unions requires a minimum of 50cm of tubing.&nbsp; Thus, mixing column is now 5x as long as it needs to be but waiting for Chris P. to do testing.&nbsp; Hope to test column next week around LLNL PCR visity.&nbsp;

ACTION:&nbsp; Jose to lengthen motor control cables (Addie).
ACTION:&nbsp; syringe motor mount.&nbsp; Mount 'upsidedown' for better lubrication.&nbsp; Changing motor for better gearing/speed ratio. (Addie)&nbsp; {color:#0000ff}DONE{color}
{color:#000000}ACTION:{color} confirm with email to Tony (Jim):&nbsp; {color:#0000ff}DONE{color}

h3. Software

Much discussion on how the code will be modified to accommodate a new thermal profile for puck heating.&nbsp; Brent suggested a very thorough plan of action, but was forced to accept a less elegant solution.&nbsp; Scott will provide nominal offsets and Brent will put in a mechanism to set gain/offset before every heating cycle.&nbsp; He has agreed to do this before the can cold-testing. (Brent)&nbsp;

Pressure tests; did four pressures.&nbsp; Chris P tried to grow lysate, but ran out of a reagent.&nbsp; We like 20-25psi---it's pumping like GG was. &nbsp; This number easy to change.&nbsp; He's made several parameters changeable.&nbsp; Chris P. knows most. &nbsp;&nbsp; Brent will create cheat-sheet for how these changes.

&nbsp;Firmware:&nbsp; servo-control works very well on MFB.&nbsp; Sampling at 64hz.&nbsp; this is different from all other dwarves so what should be do?&nbsp; Old code cannot change the divisor in the dwarves, but new Ruby can actually change the divisor, thus sampling at different rates.&nbsp; These are relatively large firmware modifications, so we will implement when the MFB goes in, NOT for Spring deployments.&nbsp;

Several small changes have resulted in a new firmware version that we +should+ update on Mack, Bruce, Neo.&nbsp; Brent will send email to everyone explaining changes.

+Action Items:+&nbsp;

ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent)
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)
ACTION:&nbsp; Update firmware on Mack, Bruce, Neo with the 'slightly modified version, and email the changes within this new firmware to everyone (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code (Brent):&nbsp; {color:#ff0000}Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress{color}
{color:#000000}ACTION:{color}&nbsp; Test pressure stuff (above); if problems, then heating stuff is dropped.&nbsp; {color:#0000ff}DONE (we believe 20-25psi delta will work like GG){color}
{color:#000000}ACTION{color}:&nbsp; Chris to give Brent water sample for running next week.&nbsp; Test running on bench at various pressures and run lysate test to test effects of different pressures (Chris/Brent) {color:#0000ff}DONE{color}

h3. Sphere and 4K DWSMS

Oil for DWSM has arrived and currenly being cold-tested.&nbsp; Doug met with local micro-pump rep, and is getting close to choosing the pumps he wants.&nbsp; All parts are ordered for the plastic model, which he will build in the Bldg B lab.&nbsp; He has the layout design and partial design for vavle actuators.&nbsp;

Nilo has inventoried all pucks and is receiving instruction on how to get them laser-etched.&nbsp; Will take first batch for etching next week.&nbsp; Following this [numbering scheme|ESPAPP:Puck Numbering System].
\\

{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
ACTION: Get quote for surface cans from Gene and place order (Jim):&nbsp; {color:#0000ff}DONE{color}
{color:#000000}ACTION{color}: discuss procurement and build schedule for next 2 cores (WHOI and CMORE funded) at 1-24-2008 mtg (in two weeks) {color:#ff0000}next meeting{color}.&nbsp;

h3. GUI Development

Kevin trying to have the Mission Script GUI in our hands before the [cold box testing.|ESPAPP:2008 Q1-Q2 Schedule]\\
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 24, 2008*

*11am-12*
Present: Jim, Doug, Scott, Addie, Kevin, Brent, Chris S.
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp; {color:#339999}Hasn't shuffled pucks yet.&nbsp; Almost finished testing{color}
* Update on valve cold-testing of MACK.&nbsp; {color:#339999}Still to begin{color}
* Jan 15-29 both Bruce & Neo to be re-valved.&nbsp; Progress? {color:#ff0000}Not begun{color} yet
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; {color:#339999}Not ready until cold-testing finished{color}
* New syringe cost.&nbsp; Acct to charge?&nbsp;&nbsp; {color:#339999}50 syringes&nbsp; \~$10K charge to 900612.&nbsp; May start to identify people that want these new syringes (Chris S.){color}
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp; {color:#339999}Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612 (look to see if he has time (Jim)&nbsp; maybe a subaccount (.99 for CIP)).{color}
* Mock deployment schedule and Spring field trials
* PROCUREMENT AND BUILD SCHEDULE FOR NEXT 2 CORES (WHOI & CMORE)

&nbsp;*Two Options for build of two more cores:*

Buy parts under another grant and then transfer charges to WHOI grant when money comes in in August 2008.&nbsp; This is dangerous as WHOI may not get money and if we've bought ahead, we'd be stuck with parts, and have hit another grant very hard.
CMORE machine will initially be stationed here at MBARI but eventually goes to CMORE partner.&nbsp; The best plan is to use BRUCE/MACK as the WHOI & CMORE machines, and have parts for their replacements on hand. &nbsp;&nbsp;

Chris thinks--do we know what we need to order.&nbsp; Get all ready to cut and look to mid-summer for procurement and build starting in Sept.&nbsp; By that time more money comes through and we could add to the purchases.&nbsp; This applies to all Jose's boards except the MFB boards.&nbsp; Now we should order enough dwarfs for MFB and spares. For MFB boards split between 701312 and 800560.&nbsp; Make sure subaccount charges are correct.&nbsp; The summer order would be the rest and the long-lead orders.&nbsp;
\\

Second MFB is parted and here.&nbsp; Chris and Jim will work with grants to make sure money is spent correctly (reallocate MOORE monies).

Neo has been capitalized so buying any more parts goes to a different account (maintenance or equipment supplies, not the NEO CIP account).&nbsp;

[Q1-Q2 2008|ESPAPP:2008 Q1-Q2 Schedule] schedule has slipped.&nbsp; Must shift our schedule back one month.&nbsp; Maybe can shave mock-deployment by running harder/faster.&nbsp;

ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp;
\\

+Action Items+

ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp; {color:#ff0000}In progress:{color}

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}

h3.


h3. MFB

Discussion Items:
* Motor control cables lengthened?&nbsp; {color:#0000ff}Finished{color}

problem in cable that goes to 3-way valve.&nbsp; Jose can't figure it out.&nbsp;

ACTION: Will work on figuring cable problem. (Addie)
* Heater block re-plumbed?&nbsp; Owner's manual written detailing new drivers?
* Begin PCR tests?.

LLNL commands are now in Ruby (via Bob Herlien) and Addie has placed on Confluence a '[users manual|ESPAPP:Micro-Fluidics Block^~$B PCR Module Users Manual V1.0.doc]' for the PCR module.&nbsp; Software works well and easy to write scripts.

Fan not working on PCR module and Addie will try and track down why (check in various terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie)

ACTION: write Tony at LLNL for advice. {color:#0000ff}FINISHED{color}&nbsp;

Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie)&nbsp;

h3. Software

* Gain/offset for heating cycles installed?&nbsp; Still trying to test
* Has 'Cheat Sheet' for new sample collection parameters been distributed? (Not done)
* Firmware updated on Mack, Bruck & Neo? still testing

+Action Items:+&nbsp;
ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent): implemented but figuring when it should happen.&nbsp;
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)
ACTION:&nbsp; Update firmware on Mack, Bruce, Neo with the 'slightly modified version, and email the changes within this new firmware to everyone (Brent) DONE

Brent will work on operational model for temp control.&nbsp; Get it ready for Sept that will be implemented with the MFB. (Brent)&nbsp;

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress{color}

h3. Sphere and 4K DWSMS

* Oil cold testing.&nbsp; Finished?&nbsp; {color:#339999}100 cst goes 150 cst when in cold.&nbsp; It's a significant increase but can be counterd by buying lower viscosity oil.{color}
* &nbsp;
* Screen drawings.&nbsp; Checked?&nbsp; Ready for order?&nbsp; Photofab drawings have been looked at and they have a new spec to send to PFI.&nbsp; The way they fabbed last time they took out too much b/w holes.&nbsp; Doug wants them etched to a certain mass.&nbsp;

ACTION:&nbsp; Scott to send samples and current idea to see if they can do it to weight. (Scott will mail samples to them)&nbsp; Chris and Roman have spec for scintered frits and are discussing how many to order.&nbsp; They have a quote.

* Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}
* DWSM progress?&nbsp;&nbsp; {color:#339999}Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.{color}

No word on sphere.&nbsp; Discussion about Tapemation machining and how we should get insurance or discuss protection.&nbsp;

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim)

{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
&nbsp;

h3. GUI Development

* Mission script progress

ACTION:&nbsp; Will try and have mission script GUI out next week.&nbsp; Kevin will meet with Chris S. (Kevin)
* Adjustment of project #'s in JIRA

ACTION: Kevin will delete one account and the one to use is ESP Gen II. {color:#0000ff}FINISHED{color}\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[# [2008 Q1-Q2 Schedule]
# [Machinist build schedule (Feb 2007)]]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
 Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop\\
 Mag bead | 3 \\ |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[h2. &nbsp;Outline of instrument plan for Jan-Jun, 2008


Mack has been cold tested with new hand and new valves and Roman Flush run to check tubing.

Temp calibration Jan 29-31.

Feb 5,6,7 Science will prep reagents, generate mission script, run sub-protocol tests&nbsp;
# One month cold test of Mack w/ his new valves/hand starting Feb 11.
## OBJECTIVE:&nbsp; get through a full carousel of pucks
## test should last most of
# &nbsp;
# &nbsp;
# &nbsp;
# &nbsp;
# and re-valve *both* Bruce and Neo (2 weeks; Jan 15-->Jan 29)
# Begin +1 month test+ in chamber with MACK  (~4 weeks; Feb 1-->Feb 25)
#- Cheri to design and construct box
#- Use fittings from deep canister
#- sample pressure pots
# Prep for Spring deployments (Feb 25-->Feb 29)
# {color:#ff0000}{*}Deploy{*}{color} MACK (March 3)
#- Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
# &nbsp;{color:#0000ff}{*}Recover{*}{color} MACK, {color:#ff0000}{*}Deploy{*}{color} BRUCE (Apr 1)
# &nbsp;{color:#0000ff}{*}Recover{*}{color} BRUCE, {color:#ff0000}{*}Deploy{*}{color} MACK (May 1)
# {color:#0000ff}{*}Recover{*}{color} MACK (May 27), {color:#ff0000}{*}Deploy{*}{color} *both* BRUCE and NEO (May 28)
# End mission Jun 30.\\ \\ \\ \\ \\ \\

(Revised 29 Jan 2008)&nbsp;]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[h2. Outline of instrument plan for Jan-Jun, 2008

# Cold Test Bruce with his new hand and re-valve Mack to new motors and mounts (2 weeks; Dec 31--->Jan 15)
\\
# Cold test Mack w/ his new valves/hand and re-valve *both* Bruce and Neo (2 weeks; Jan 15-->Jan 29)
# Begin +1 month test+ in chamber with MACK  (~4 weeks; Feb 1-->Feb 25)
#- Cheri to design and construct box
#- Use fittings from deep canister
#- sample pressure pots
# Prep for Spring deployments (Feb 25-->Feb 29)
# {color:#ff0000}{*}Deploy{*}{color} MACK (March 3)
#- Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
# &nbsp;{color:#0000ff}{*}Recover{*}{color} MACK, {color:#ff0000}{*}Deploy{*}{color} BRUCE (Apr 1)
# &nbsp;{color:#0000ff}{*}Recover{*}{color} BRUCE, {color:#ff0000}{*}Deploy{*}{color} MACK (May 1)
# {color:#0000ff}{*}Recover{*}{color} MACK (May 27), {color:#ff0000}{*}Deploy{*}{color} *both* BRUCE and NEO (May 28)
# End mission Jun 30.]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | * Microsonic \\
w/ w.o beads
* Magnet flipper
* Bead Mill
* Grinder | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | * Qiagen Membrane\\
 Single use only\\
 Mock up on MFB\\
 May need a pressure sensor
* iFast\\
 May or may not be renewable\\
 Currently using RLT\\
 For DA: pass beads to SPR\\
 For NA: no beads pass
* Current silica column\\
 Renewable
*  | 4 |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | DNA/RNA:\\
 * (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* &nbsp;(2) Heat | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
*  | 3\\ |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 31, 2008*

*11am-12*
Present:
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp; {color:#339999}Hasn't shuffled pucks yet.&nbsp; Almost finished testing{color}
* Update on valve cold-testing of MACK.&nbsp; {color:#339999}Still to begin{color}
* Jan 15-29 both Bruce & Neo to be re-valved.&nbsp; Progress? {color:#ff0000}Not begun{color} yet
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; {color:#339999}Not ready until cold-testing finished{color}
* New syringe cost.&nbsp; Acct to charge?&nbsp;&nbsp; {color:#339999}50 syringes&nbsp; \~$10K charge to 900612.&nbsp; May start to identify people that want these new syringes (Chris S.){color}
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp; {color:#339999}Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612 (look to see if he has time (Jim)&nbsp; maybe a subaccount (.99 for CIP)).{color}
* Mock deployment schedule and Spring field trials
* PROCUREMENT AND BUILD SCHEDULE FOR NEXT 2 CORES (WHOI & CMORE)

&nbsp;*Two Options for build of two more cores:*

Buy parts under another grant and then transfer charges to WHOI grant when money comes in in August 2008.&nbsp; This is dangerous as WHOI may not get money and if we've bought ahead, we'd be stuck with parts, and have hit another grant very hard.
CMORE machine will initially be stationed here at MBARI but eventually goes to CMORE partner.&nbsp; The best plan is to use BRUCE/MACK as the WHOI & CMORE machines, and have parts for their replacements on hand. &nbsp;&nbsp;

Chris thinks--do we know what we need to order.&nbsp; Get all ready to cut and look to mid-summer for procurement and build starting in Sept.&nbsp; By that time more money comes through and we could add to the purchases.&nbsp; This applies to all Jose's boards except the MFB boards.&nbsp; Now we should order enough dwarfs for MFB and spares. For MFB boards split between 701312 and 800560.&nbsp; Make sure subaccount charges are correct.&nbsp; The summer order would be the rest and the long-lead orders.&nbsp;
\\

Second MFB is parted and here.&nbsp; Chris and Jim will work with grants to make sure money is spent correctly (reallocate MOORE monies).

Neo has been capitalized so buying any more parts goes to a different account (maintenance or equipment supplies, not the NEO CIP account).&nbsp;

Q1-Q2 2008 schedule has slipped.&nbsp; Must shift our schedule back one month.&nbsp; Maybe can shave mock-deployment by running harder/faster.&nbsp;

ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp;
\\

+Action Items+

ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp; {color:#0000ff}Finished{color}

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#0000ff}Finished{color}

h3.


h3. MFB

Discussion Items:

ACTION: Will work on figuring cable problem to three-way valves. (Addie)
ACTION: Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie) {color:#0000ff}Finished{color}

h3.

* Heater block re-plumbed?&nbsp; Owner's manual written detailing new drivers?
* Begin PCR tests?.

LLNL commands are now in Ruby (via Bob Herlien) and Addie has placed on Confluence a 'users manual' for the PCR module.&nbsp; Software works well and easy to write scripts.

Fan not working on PCR module and Addie will try and track down why (check in various terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie); {color:#0000ff}Finished{color}

ACTION: write Tony at LLNL for advice. {color:#0000ff}FINISHED{color}&nbsp;

h3. Software

* Gain/offset for heating cycles installed?&nbsp; Still trying to test
* Has 'Cheat Sheet' for new sample collection parameters been distributed? (Not done)
* Firmware updated on Mack, Bruck & Neo? still testing

+Action Items:+&nbsp;
ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent): implemented but figuring when it should happen.&nbsp;
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)
ACTION:&nbsp; Update firmware on Mack, Bruce, Neo with the 'slightly modified version, and email the changes within this new firmware to everyone (Brent) DONE

Brent will work on operational model for temp control.&nbsp; Get it ready for Sept that will be implemented with the MFB. (Brent)&nbsp;

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress{color}

h3. Sphere and 4K DWSMS

* Oil cold testing.&nbsp; Finished?&nbsp; {color:#339999}100 cst goes 150 cst when in cold.&nbsp; It's a significant increase but can be counterd by buying lower viscosity oil.{color}
* &nbsp;
* Screen drawings.&nbsp; Checked?&nbsp; Ready for order?&nbsp; Photofab drawings have been looked at and they have a new spec to send to PFI.&nbsp; The way they fabbed last time they took out too much b/w holes.&nbsp; Doug wants them etched to a certain mass.&nbsp;

ACTION:&nbsp; Scott to send samples and current idea to see if they can do it to weight. (Scott will mail samples to them)&nbsp; Chris and Roman have spec for scintered frits and are discussing how many to order.&nbsp; They have a quote.
* Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}
* DWSM progress?&nbsp;&nbsp; {color:#339999}Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.{color}

No word on sphere.&nbsp; Discussion about Tapemation machining and how we should get insurance or discuss protection.&nbsp;

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim)

{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
&nbsp;

h3. GUI Development

* Mission script progress

ACTION:&nbsp; Will try and have mission script GUI out next week.&nbsp; Kevin will meet with Chris S. (Kevin)
* Adjustment of project #'s in JIRA

ACTION: Kevin will delete one account and the one to use is ESP Gen II. {color:#0000ff}FINISHED{color}\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h3. A. [Cawthron Planning Document]


h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)]]></property>
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<property name="body"><![CDATA[h3. A. [Cawthron Planning Document]


h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)
\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system. ]]></property>
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h3. [Cawthron Planning Document]]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

h4. {color:#ff00cc}Puget Sound{color}

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm ]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ | 4 |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans.\\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | Possible Mfg's | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ | 4 |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}MAKAI flight w 4 Archives, 1 Lyse-n-go{color}

*Feb 2-4, 2016*

Repeat of Dec flight.&nbsp; Here are notes from Yanwu's summary:

(Note: when reaching each target depth (peak-chl or pre-set), we give Makai 10 minutes to damp down depth undulation.)

Sample#1 (lyse&go sample. At chl peak):
Makai descended from surface, found the chl peak at 8.7m. On the ensuing ascent, Makai held depth at 8.7m, and triggered sample#1.
Took 63 minutes to complete.&nbsp; Then Makai surfaced to "report to shore".

Sample#2 (archive sample. At chl peak):
Makai descended from surface, found the chl peak at 12.7m. On the ensuing ascent, Makai held depth at 12.3m, and triggered sample#2. (Note: the water column was quite mixed vertically. The chl values at 8m and 12m were very close. Makai was doing her best to pick the relatively weak peak.)&nbsp; Took 41 minutes to complete.

Sample#3 (archive sample. At reacquired chl peak):
In order to reacquire the chl peak (considering the peak-chl layer may have moved up or down), Makai intentionally wiggled up and down (up first, then down, and then up). On the "down", it found the chl peak at 13.2m. On the ensuing "up", Makai held depth at 13.0m, and triggered sample#3.&nbsp; Took 40 minutes to complete.

Sample#4 (archive sample. At pre-set 27m. Control sample.):
Makai dove to the pre-set 27m depth, and triggered sample#4.&nbsp; Took 39 minutes to complete.

Sample#5 (archive sample. At pre-set 27m. Control sample.):
Makai stayed at the pre-set 27m depth, and triggered sample#5.&nbsp; Took 38 minutes to complete.

h4. {color:#ff00cc}Del Mar--ESP-Waldo{color}

*May 17, 2016*

Used M/V Merlin (Walt Crampton), with MBARI surface mooring.&nbsp; Divers from SCRIPPS.&nbsp; Deployed with CTD about 400 yds from Del Mar mooring (SE of their mooring). Used new anchor line, #1 shockle, and 35m EM cable.

Ship coordinates when we dropped it:&nbsp; 32' 55.603N&nbsp; 117' 18.895W


Melo coordinates (IMEI: 300034012090780):&nbsp; 32.92633 \-117.31491

Water depth 100m.&nbsp; Divers reported master link at 22.8m, can top at 16.76m.&nbsp; CTD reading \~18m. ]]></property>
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# [10Jan2008]
# [17Jan2008]]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}MAKAI flight w 4 Archives, 1 Lyse-n-go{color}

*Feb 2-4, 2016*

Repeat of Dec flight.&nbsp; Here are notes from Yanwu's summary:

(Note: when reaching each target depth (peak-chl or pre-set), we give Makai 10 minutes to damp down depth undulation.)

Sample#1 (lyse&go sample. At chl peak):
Makai descended from surface, found the chl peak at 8.7m. On the ensuing ascent, Makai held depth at 8.7m, and triggered sample#1.
Took 63 minutes to complete.&nbsp; Then Makai surfaced to "report to shore".

Sample#2 (archive sample. At chl peak):
Makai descended from surface, found the chl peak at 12.7m. On the ensuing ascent, Makai held depth at 12.3m, and triggered sample#2. (Note: the water column was quite mixed vertically. The chl values at 8m and 12m were very close. Makai was doing her best to pick the relatively weak peak.)&nbsp; Took 41 minutes to complete.

Sample#3 (archive sample. At reacquired chl peak):
In order to reacquire the chl peak (considering the peak-chl layer may have moved up or down), Makai intentionally wiggled up and down (up first, then down, and then up). On the "down", it found the chl peak at 13.2m. On the ensuing "up", Makai held depth at 13.0m, and triggered sample#3.&nbsp; Took 40 minutes to complete.

Sample#4 (archive sample. At pre-set 27m. Control sample.):
Makai dove to the pre-set 27m depth, and triggered sample#4.&nbsp; Took 39 minutes to complete.

Sample#5 (archive sample. At pre-set 27m. Control sample.):
Makai stayed at the pre-set 27m depth, and triggered sample#5.&nbsp; Took 38 minutes to complete. ]]></property>
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<property name="body"><![CDATA[h4. (as of April, 2015)


h1. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

*21.5m (BAD)*
Now with bad connector...&nbsp;
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos in the attachments of this page.
* late-2014; was this EM cable repaired?

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)

*15.2m (BAD; bad BSR?)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]
\\

All shockles modified Dec 2015 to be like 001 (stretchier cords)

h4. ESP-001 (modified with 'stretchier' cord)

* 44 days during Catalina (April 2014) deployment
* Moran MB deployment (Sep/Oct 2014)
* ECOHAB?

h4. ESP-002


h4. ESP-003


h4. ESP-004


h4. ESP-005


h1. Anchor lines

\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4.


h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\
\\]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}MAKAI flight w 4 Archives, 1 Lyse-n-go{color}

*Feb 2-4, 2016*

Repeat of Dec flight.&nbsp; Here are notes from Yanwu's summary:

(Note: when reaching each target depth (peak-chl or pre-set), we give Makai 10 minutes to damp down depth undulation.)

Sample#1 (lyse&go sample. At chl peak):
Makai descended from surface, found the chl peak at 8.7m. On the ensuing ascent, Makai held depth at 8.7m, and triggered sample#1.
Took 63 minutes to complete.&nbsp; Then Makai surfaced to "report to shore".

Sample#2 (archive sample. At chl peak):
Makai descended from surface, found the chl peak at 12.7m. On the ensuing ascent, Makai held depth at 12.3m, and triggered sample#2. (Note: the water column was quite mixed vertically. The chl values at 8m and 12m were very close. Makai was doing her best to pick the relatively weak peak.)&nbsp; Took 41 minutes to complete.

Sample#3 (archive sample. At reacquired chl peak):
In order to reacquire the chl peak (considering the peak-chl layer may have moved up or down), Makai intentionally wiggled up and down (up first, then down, and then up). On the "down", it found the chl peak at 13.2m. On the ensuing "up", Makai held depth at 13.0m, and triggered sample#3.&nbsp; Took 40 minutes to complete.

Sample#4 (archive sample. At pre-set 27m. Control sample.):
Makai dove to the pre-set 27m depth, and triggered sample#4.&nbsp; Took 39 minutes to complete.

Sample#5 (archive sample. At pre-set 27m. Control sample.):
Makai stayed at the pre-set 27m depth, and triggered sample#5.&nbsp; Took 38 minutes to complete.

h4. {color:#ff00cc}Del Mar--ESP-Waldo{color}

*May 17, 2016*

Used M/V Merlin (Walt Crampton), with MBARI surface mooring.&nbsp; Divers from SCRIPPS.&nbsp; Deployed with CTD about 400 yds from Del Mar mooring (SE of their mooring). Used new anchor line, #1 shockle, and 35m EM cable.


&nbsp;Melo coordinates (IMEI: 300034012090780):&nbsp; 32.92633 \-117.31491
\\ \\]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.12|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.3%2028_12_2007.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram12-19-07.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 24, 2008*

*11am-12*
Present:\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing
* Update on valve cold-testing of MACK
* Jan 15-29 both Bruce & Neo to be re-valved.&nbsp; Progress?
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?
* New syringe cost.&nbsp; Acct to charge?
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?
* PROCUREMENT AND BUILD SCHEDULE FOR NEXT 2 CORES (WHOI & CMORE)

+Action Items+

ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp;

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}

h3.


h3. MFB

Discussion Items:
* Motor control cables lengthened?
* Heater block re-plumbed?&nbsp; Owner's manual written detailing new drivers?
* Begin PCR tests?

h3. Software

* Gain/offset for heating cycles installed?
* Has 'Cheat Sheet' for new sample collection parameters been distributed?
* Firmware updated on Mack, Bruck & Neo?

+Action Items:+&nbsp;
ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent)
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)
ACTION:&nbsp; Update firmware on Mack, Bruce, Neo with the 'slightly modified version, and email the changes within this new firmware to everyone (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code (Brent):&nbsp; {color:#ff0000}Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress{color}

h3. Sphere and 4K DWSMS

* Oil cold testing.&nbsp; Finished?
* Screen drawings.&nbsp; Checked?&nbsp; Ready for order?
* Battery boxes?
* DWSM progress?&nbsp;

{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
{color:#000000}ACTION{color}: discuss procurement and build schedule for next 2 cores (WHOI and CMORE funded) at 1-24-2008 mtg (in two weeks) {color:#ff0000}next meeting{color}.&nbsp;

h3. GUI Development

* Mission script progress

\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.2|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.3%2028_12_2007.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram12-19-07.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 24, 2008*

*11am-12*
Present:

AGENDA STILL TO COME. &nbsp;&nbsp;

h3. Tech Transfer


h6. Discussion Items:

* Arm status update
* Environmental test chamber update

*Arm/Hand*.&nbsp; Removed Bruce from cold testing, and _almost{_}finished with hand cold testing.&nbsp; Removed hand from Bruce and installed on Mack. Plan is to finish cold-test on hand and cold-test valves simultaneously on Mack.&nbsp; First priority in cold is to finish testing hand gripper.&nbsp; Once it passes, Mike will get green-light parts of the other hands (first 3 old action items).&nbsp; Order is placed with Maxxon for new forearm motors (maybe 6-8 weeks).&nbsp; Small order of fluidic fittings still needed for all of them.&nbsp; (Cheri)

*ETC* (Environmental Test Chamber).&nbsp; Cold box finished, electrical connectors in, fluidic connectors still need to be put in.&nbsp; New rotary valves all on Mack and being homed and calibrated.&nbsp; All we be ready for cold testing by end of day.

+Action Items+

ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp;

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}



h3.


h3. MFB

Discussion Items:

•&nbsp;&nbsp;&nbsp; Syringe positioning

Syringe now oriented like other syringes on the core, i.e., pointing 'downward', and working well.&nbsp; Still waiting to test as several cables needed to be lengthened.

•&nbsp;&nbsp;&nbsp; Status of mixing column for extraction lysate.

Unable to build a 10cm mixing column because the use of 2 reducing unions requires a minimum of 50cm of tubing.&nbsp; Thus, mixing column is now 5x as long as it needs to be but waiting for Chris P. to do testing.&nbsp; Hope to test column next week around LLNL PCR visity.&nbsp;

ACTION:&nbsp; Jose to lengthen motor control cables (Addie).



h3. Software

Much discussion on how the code will be modified to accommodate a new thermal profile for puck heating.&nbsp; Brent suggested a very thorough plan of action, but was forced to accept a less elegant solution.&nbsp; Scott will provide nominal offsets and Brent will put in a mechanism to set gain/offset before every heating cycle.&nbsp; He has agreed to do this before the can cold-testing. (Brent)&nbsp;

Pressure tests; did four pressures.&nbsp; Chris P tried to grow lysate, but ran out of a reagent.&nbsp; We like 20-25psi---it's pumping like GG was. &nbsp; This number easy to change.&nbsp; He's made several parameters changeable.&nbsp; Chris P. knows most. &nbsp;&nbsp; Brent will create cheat-sheet for how these changes.

&nbsp;Firmware:&nbsp; servo-control works very well on MFB.&nbsp; Sampling at 64hz.&nbsp; this is different from all other dwarves so what should be do?&nbsp; Old code cannot change the divisor in the dwarves, but new Ruby can actually change the divisor, thus sampling at different rates.&nbsp; These are relatively large firmware modifications, so we will implement when the MFB goes in, NOT for Spring deployments.&nbsp;

Several small changes have resulted in a new firmware version that we +should+ update on Mack, Bruce, Neo.&nbsp; Brent will send email to everyone explaining changes.

+Action Items:+&nbsp;

ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent)
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)
ACTION:&nbsp; Update firmware on Mack, Bruce, Neo with the 'slightly modified version, and email the changes within this new firmware to everyone (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code (Brent):&nbsp; {color:#ff0000}Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress{color}


h3. Sphere and 4K DWSMS

Oil for DWSM has arrived and currenly being cold-tested.&nbsp; Doug met with local micro-pump rep, and is getting close to choosing the pumps he wants.&nbsp; All parts are ordered for the plastic model, which he will build in the Bldg B lab.&nbsp; He has the layout design and partial design for vavle actuators.&nbsp;

Nilo has inventoried all pucks and is receiving instruction on how to get them laser-etched.&nbsp; Will take first batch for etching next week.&nbsp; Following this numbering scheme.
\\

{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
{color:#000000}ACTION{color}: discuss procurement and build schedule for next 2 cores (WHOI and CMORE funded) at 1-24-2008 mtg (in two weeks) {color:#ff0000}next meeting{color}.&nbsp;

h3. GUI Development

Kevin trying to have the Mission Script GUI in our hands before the cold box testing.\\
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.3|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.3%2028_12_2007.doc]
# [PCR Users Manual v1.0|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20PCR%20Users%20Manual%20V1.0%20.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram12-19-07.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.3|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.3%2028_12_2007.doc]
# [PCR Users Manual v1.0|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20PCR%20Module%20Users%20Manual%20V1.0%20.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram12-19-07.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a spreadsheet that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.3|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.3%2028_12_2007.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram12-19-07.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.3|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.3%2028_12_2007.doc]
# [PCR Users Manual v1.0|^~$B PCR Module Users Manual V1.0.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram12-19-07.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.3|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.3%2028_12_2007.doc]
# [PCR Users Manual v1.0|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20PCR%20Users%20Manual%20V1.0.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram12-19-07.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 24, 2008*

*11am-12*
Present: Jim, Doug, Scott, Addie, Kevin,
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp; Hasn't shuffled pucks yet.&nbsp; Almost finishedtesting
* Update on valve cold-testing of MACK.&nbsp; Still to begin
* Jan 15-29 both Bruce & Neo to be re-valved.&nbsp; Progress? Not begun yet
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; Not ready until cold-testing finished
* New syringe cost.&nbsp; Acct to charge?&nbsp;&nbsp; 50 syringes&nbsp; \~$10K charge to 900612.&nbsp; May start to identify people that want these new syringes (Chris S.)
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp; Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612 (look to see if he has time (Jim)&nbsp; maybe a subaccount (.99 for CIP)).
* Mock deployment schedule and Spring field trials
* PROCUREMENT AND BUILD SCHEDULE FOR NEXT 2 CORES (WHOI & CMORE)

&nbsp;Two Options:

buy parts under another grant and then transfer to WHOI grant.&nbsp; We are expecting to get this money in August.&nbsp; this is dangerous as WHOI may NOT get money and if we've bought ahead, we'd be stuck with parts, and have hit another grant very hard.&nbsp; We would be making bruce/mack for WHOI and then have parts for a second machine once this is delivered.

CMORE machine will initially be here but goes to cmore partner.&nbsp; Probably will use bruce/mack and make it the CMORE machine. &nbsp;&nbsp;

Chris thinks--do we know what we need to order.&nbsp; Get all ready to cut and look to mid-summer for procurement and build starting in Sept.&nbsp; By that time more money comes through and we could add to the purchases.&nbsp; This applies to all Jose's boards except the MFB boards.&nbsp; Now is enough dwarfs for MFB and spares. for MFB split between 701312 and 800560.&nbsp; make sure subaccount charges are correct.&nbsp; The summer order would be the rest and the long-lead orders.&nbsp;\\

Second MFB is parted and here.&nbsp; Chris and Jim will work with grants to make sure money is spent

Neo has been capitalized so buying a nother part goes to a different account (maintenance or equipment supplies, not the NEO CIP account).&nbsp;

whole system hasn't shufiftfled pucks.&nbsp;

Must shift our schedule back one month.&nbsp; Maybe can shave mock-deployment by running harder/faster.&nbsp;

ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp;
\\

+Action Items+

ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp;

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}

h3.


h3. MFB

Discussion Items:
* Motor control cables lengthened?&nbsp; Finished

problem in cable that goes to 3-way valve.&nbsp; Jose can't figure it out.&nbsp; Work on it. (Addie)
* Heater block re-plumbed?&nbsp; Owner's manual written detailing new drivers?
* Begin PCR tests?.

LLNL commands are now in Ruby (via Bob Herlien) and Addie has placed on Confluence a 'users manual' for the PCR module.&nbsp; Software works well and easy to write scripts.

Fan not working on PCR module and Addie will try and track down why (check in vrious terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie)

Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie)&nbsp;

h3. Software

* Gain/offset for heating cycles installed?&nbsp; Still trying to test
* Has 'Cheat Sheet' for new sample collection parameters been distributed? (Not done)
* Firmware updated on Mack, Bruck & Neo? still testing

+Action Items:+&nbsp;
ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent): implemented but figuring when it should happen.&nbsp;
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)
ACTION:&nbsp; Update firmware on Mack, Bruce, Neo with the 'slightly modified version, and email the changes within this new firmware to everyone (Brent) DONE

Brent will work on operational model for temp control.&nbsp; Get it ready for Sept that will be implemented with the MFB. (Brent)&nbsp;

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress{color}

h3. Sphere and 4K DWSMS

* Oil cold testing.&nbsp; Finished?&nbsp; 100 cst goes 150 cst when in cold.&nbsp; It's a significant but buy new lower viscosity.
* &nbsp;
* Screen drawings.&nbsp; Checked?&nbsp; Ready for order?&nbsp; Photofab drawings have been looked at and they have a new spec they are sending to PFI.&nbsp; The way they fabbed last time they took out too much b/w holes.&nbsp; Doug wants them etched to a certain mass.&nbsp; Scott to send samples and current idea to see if they can do it to weight. (Scott will mail samples to them)&nbsp; Chris and Roman have spec for scintered frits and are discussing how many to order.&nbsp; They have a quote.
* &nbsp;
* Battery boxes?&nbsp; Scott still waiting to hear.
* DWSM progress?&nbsp;&nbsp; Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.

No word on sphere.&nbsp; Discussion about Tapemation machining and how we should get insurance or discuss protection.&nbsp;

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim)


{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
&nbsp;

h3. GUI Development

* Mission script progress
* Adjustment of project #'s in JIRA

\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 24, 2008*

*11am-12*
Present: Jim, Doug, Scott, Addie, Kevin,
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp; Hasn't shuffled pucks yet.&nbsp; Almost finishedtesting
* Update on valve cold-testing of MACK.&nbsp; Still to begin
* Jan 15-29 both Bruce & Neo to be re-valved.&nbsp; Progress? Not begun yet
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; Not ready until cold-testing finished
* New syringe cost.&nbsp; Acct to charge?&nbsp;&nbsp; 50 syringes&nbsp; \~$10K charge to 900612.&nbsp; May start to identify people that want these new syringes (Chris S.)
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp; Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612 (look to see if he has time (Jim)&nbsp; maybe a subaccount (.99 for CIP)).
* Mock deployment schedule and Spring field trials
* PROCUREMENT AND BUILD SCHEDULE FOR NEXT 2 CORES (WHOI & CMORE)

&nbsp;Two Options:

buy parts under another grant and then transfer to WHOI grant.&nbsp; We are expecting to get this money in August.&nbsp; this is dangerous as WHOI may NOT get money and if we've bought ahead, we'd be stuck with parts, and have hit another grant very hard.&nbsp; We would be making bruce/mack for WHOI and then have parts for a second machine once this is delivered.

CMORE machine will initially be here but goes to cmore partner.&nbsp; Probably will use bruce/mack and make it the CMORE machine. &nbsp;&nbsp;

Chris thinks--do we know what we need to order.&nbsp; Get all ready to cut and look to mid-summer for procurement and build starting in Sept.&nbsp; By that time more money comes through and we could add to the purchases.&nbsp; This applies to all Jose's boards except the MFB boards.&nbsp; Now is enough dwarfs for MFB and spares. for MFB split between 701312 and 800560.&nbsp; make sure subaccount charges are correct.&nbsp; The summer order would be the rest and the long-lead orders.&nbsp;
\\

Second MFB is parted and here.&nbsp; Chris and Jim will work with grants to make sure money is spent

Neo has been capitalized so buying a nother part goes to a different account (maintenance or equipment supplies, not the NEO CIP account).&nbsp;

whole system hasn't shufiftfled pucks.&nbsp;

Must shift our schedule back one month.&nbsp; Maybe can shave mock-deployment by running harder/faster.&nbsp;

ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp;
\\

+Action Items+

ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp;

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}

h3.


h3. MFB

Discussion Items:
* Motor control cables lengthened?&nbsp; Finished

problem in cable that goes to 3-way valve.&nbsp; Jose can't figure it out.&nbsp; Work on it. (Addie)
* Heater block re-plumbed?&nbsp; Owner's manual written detailing new drivers?
* Begin PCR tests?.

LLNL commands are now in Ruby (via Bob Herlien) and Addie has placed on Confluence a 'users manual' for the PCR module.&nbsp; Software works well and easy to write scripts.

Fan not working on PCR module and Addie will try and track down why (check in vrious terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie)

Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie)&nbsp;

h3. Software

* Gain/offset for heating cycles installed?&nbsp; Still trying to test
* Has 'Cheat Sheet' for new sample collection parameters been distributed? (Not done)
* Firmware updated on Mack, Bruck & Neo? still testing

+Action Items:+&nbsp;
ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent): implemented but figuring when it should happen.&nbsp;
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)
ACTION:&nbsp; Update firmware on Mack, Bruce, Neo with the 'slightly modified version, and email the changes within this new firmware to everyone (Brent) DONE

Brent will work on operational model for temp control.&nbsp; Get it ready for Sept that will be implemented with the MFB. (Brent)&nbsp;

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress{color}

h3. Sphere and 4K DWSMS

* Oil cold testing.&nbsp; Finished?&nbsp; 100 cst goes 150 cst when in cold.&nbsp; It's a significant but buy new lower viscosity.
* &nbsp;
* Screen drawings.&nbsp; Checked?&nbsp; Ready for order?&nbsp; Photofab drawings have been looked at and they have a new spec they are sending to PFI.&nbsp; The way they fabbed last time they took out too much b/w holes.&nbsp; Doug wants them etched to a certain mass.&nbsp; Scott to send samples and current idea to see if they can do it to weight. (Scott will mail samples to them)&nbsp; Chris and Roman have spec for scintered frits and are discussing how many to order.&nbsp; They have a quote.
* &nbsp;
* Battery boxes?&nbsp; Scott still waiting to hear.
* DWSM progress?&nbsp;&nbsp; Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.

No word on sphere.&nbsp; Discussion about Tapemation machining and how we should get insurance or discuss protection.&nbsp;

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim)

{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
&nbsp;

h3. GUI Development

* Mission script progress

Will try and have it out next week.&nbsp; Will meet with Chris S.
* Adjustment of project #'s in JIRA

Kevin will delete one account and the one to use is ESP Gen II
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 24, 2008*

*11am-12*
Present:
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing
* Update on valve cold-testing of MACK
* Jan 15-29 both Bruce & Neo to be re-valved.&nbsp; Progress?
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?
* New syringe cost.&nbsp; Acct to charge?
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?
* Mock deployment schedule and Spring field trials
* PROCUREMENT AND BUILD SCHEDULE FOR NEXT 2 CORES (WHOI & CMORE)

+Action Items+

ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp;

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}

h3.


h3. MFB

Discussion Items:
* Motor control cables lengthened?
* Heater block re-plumbed?&nbsp; Owner's manual written detailing new drivers?
* Begin PCR tests?

h3. Software

* Gain/offset for heating cycles installed?
* Has 'Cheat Sheet' for new sample collection parameters been distributed?
* Firmware updated on Mack, Bruck & Neo?

+Action Items:+&nbsp;
ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent)
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)
ACTION:&nbsp; Update firmware on Mack, Bruce, Neo with the 'slightly modified version, and email the changes within this new firmware to everyone (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code (Brent):&nbsp; {color:#ff0000}Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress{color}

h3. Sphere and 4K DWSMS

* Oil cold testing.&nbsp; Finished?
* Screen drawings.&nbsp; Checked?&nbsp; Ready for order?
* Battery boxes?
* DWSM progress?&nbsp;

{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
{color:#000000}ACTION{color}: discuss procurement and build schedule for next 2 cores (WHOI and CMORE funded) at 1-24-2008 mtg (in two weeks) {color:#ff0000}next meeting{color}.&nbsp;

h3. GUI Development

* Mission script progress
* Adjustment of project #'s in JIRA

\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 24, 2008*

*11am-12*
Present: Jim, Doug, Scott, Addie, Kevin,
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp; Hasn't shuffled pucks yet.&nbsp; Almost finishedtesting
* Update on valve cold-testing of MACK.&nbsp; Still to begin
* Jan 15-29 both Bruce & Neo to be re-valved.&nbsp; Progress? Not begun yet
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; Not ready until cold-testing finished
* New syringe cost.&nbsp; Acct to charge?&nbsp;&nbsp; 50 syringes&nbsp; \~$10K charge to 900612.&nbsp; May start to identify people that want these new syringes (Chris S.)
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp; Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612 (look to see if he has time (Jim)&nbsp; maybe a subaccount (.99 for CIP)).
* Mock deployment schedule and Spring field trials
* PROCUREMENT AND BUILD SCHEDULE FOR NEXT 2 CORES (WHOI & CMORE)

&nbsp;Two Options:

buy parts under another grant and then transfer to WHOI grant.&nbsp; We are expecting to get this money in August.&nbsp; this is dangerous as WHOI may NOT get money and if we've bought ahead, we'd be stuck with parts, and have hit another grant very hard.&nbsp; We would be making bruce/mack for WHOI and then have parts for a second machine once this is delivered.


CMORE machine will initially be here but goes to cmore partner.&nbsp; Probably will use bruce/mack and make it the CMORE machine. &nbsp;&nbsp;

Chris thinks--do we know what we need to order.&nbsp; Get all ready to cut and look to mid-summer for procurement and build starting in Sept.&nbsp; By that time more money comes through and we could add to the purchases.&nbsp; This applies to all Jose's boards except the MFB boards.&nbsp; Now is enough dwarfs for MFB and spares.&nbsp; The summer order would be the rest and the long-lead orders.&nbsp;

whole system hasn't shufiftfled pucks.&nbsp;

Must shift our schedule back one month.&nbsp; Maybe can shave mock-deployment by running harder/faster.&nbsp;


ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp;\\

+Action Items+

ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp;

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#ff0000}In progress{color}

h3.


h3. MFB

Discussion Items:
* Motor control cables lengthened?&nbsp; Finished

problem in cable that goes to 3-way valve.&nbsp; Jose can't figure it out.&nbsp; Work on it. (Addie)
* Heater block re-plumbed?&nbsp; Owner's manual written detailing new drivers?
* Begin PCR tests?.

LLNL commands are now in Ruby (via Bob Herlien) and Addie has placed on Confluence a 'users manual' for the PCR module.&nbsp; Software works well and easy to write scripts.


Fan not working on PCR module and Addie will try and track down why (check in vrious terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie)


Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie)&nbsp;

h3. Software

* Gain/offset for heating cycles installed?
* Has 'Cheat Sheet' for new sample collection parameters been distributed?
* Firmware updated on Mack, Bruck & Neo?

+Action Items:+&nbsp;
ACTION:&nbsp; Put in mechanism for setting gain/offset before heating cycles (Brent)
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)
ACTION:&nbsp; Update firmware on Mack, Bruce, Neo with the 'slightly modified version, and email the changes within this new firmware to everyone (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent): {color:#ff0000}Not started{color}
ACTION:&nbsp; Work with the auto-cal code (Brent):&nbsp; {color:#ff0000}Not started{color}
ACTION:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; (Jim): {color:#ff0000}In progress{color}

h3. Sphere and 4K DWSMS

* Oil cold testing.&nbsp; Finished?
* Screen drawings.&nbsp; Checked?&nbsp; Ready for order?
* Battery boxes?
* DWSM progress?&nbsp;

{color:#000000}ACTION:{color}&nbsp; get inventory of screens from Roman (Jim): Must spec hole size and fix original drawings and talk to manufacturer before ordering.&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price
{color:#000000}ACTION{color}: discuss procurement and build schedule for next 2 cores (WHOI and CMORE funded) at 1-24-2008 mtg (in two weeks) {color:#ff0000}next meeting{color}.&nbsp;

h3. GUI Development

* Mission script progress
* Adjustment of project #'s in JIRA

\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS |
| ISOLATION \\ | \\ | \\ | \\ |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | |
| Cartridge array valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | |
| Cartridge Selection Valves \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | |
| Sea Pressure fittings \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | |
| Cartridge Seals\\ | | | |
| | | | |
| FILTER | \\ | \\ | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ |
| Sample purify | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ |
| \\ | | \\ | \\ |
| | | | |
| Rotating Assembly \\ | | | |
| Rotation Mechanism \\ | | | |
| | | | |
| Cartridge Actuators \\ | | | |
| \\ | \\ | \\ | \\ |
| Cartridge Waste Collector | \\ | \\ | \\ |
| Waste Storage | | | |
| | | | |
| TRANSFER TO AM | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | |
| AM Selector Injection Loop \\ | | | |
| Clean Injection Loop \\ | | | |
| | | | |
| LRAUV Platform Interface \\ | | | |
| | | | |
Stop]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS |
| ISOLATION \\ | \\ | \\ | \\ |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | |
| Cartridge array valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | |
| Cartridge Selection Valves \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | |
| Sea Pressure fittings \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | |
| Cartridge Seals \\ | | | |
| | | | |
| \\ | \\ | \\ | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ |
| Filter Evacuate\\ | | | |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ |
| Direct Capture\\ | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ |
| | | | |
| Rotating Assembly \\ | | | |
| Rotation Mechanism \\ | | | |
| | | | |
| Cartridge Actuators \\ | | | |
| \\ | \\ | \\ | \\ |
| Cartridge Waste Collector | \\ | \\ | \\ |
| Waste Storage | | | |
| | | | |
| TRANSFER TO AM | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | |
| AM Selector Injection Loop \\ | | | |
| Clean Injection Loop \\ | | | |
| | | | |
| LRAUV Platform Interface \\ | | | |
| | | | |
Stop]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS |
| ISOLATION \\ | \\ | \\ | \\ |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | |
| Cartridge array valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | |
| Cartridge Selection Valves \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | |
| Sea Pressure fittings \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | |
| | | | |
| FILTER | \\ | \\ | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ |
| Sample purify | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ |
| \\ | | \\ | \\ |
| \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ |
| | | | |
| | | | |
| TRANSFER TO AM | | | |
| Cartridge to AM Selector\\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | |
| AM Selector Injection Loop\\ | | | |
| Clean Injection Loop\\ | | | |
| | | | |
| LRAUV Platform Interface\\ | | | |
| | | | |
Stop]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS |
| ISOLATION \\ | \\ | \\ | \\ |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | |
| Cartridge array valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | |
| Cartridge Selection Valves \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | |
| Sea Pressure fittings \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | |
| | | | |
| FILTER | \\ | \\ | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ |
| Sample purify | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ |
| \\ | | \\ | \\ |
| | | | |
| Rotating Assembly\\ | | | |
| Rotation Mechanism\\ | | | |
| | | | |
| Cartridge Actuators\\ | | | |
| \\ | \\ | \\ | \\ |
| Cartridge Waste Collector | \\ | \\ | \\ |
| Waste Storage | | | |
| | | | |
| TRANSFER TO AM | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | |
| AM Selector Injection Loop \\ | | | |
| Clean Injection Loop \\ | | | |
| | | | |
| LRAUV Platform Interface \\ | | | |
| | | | |
Stop]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">18579937</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">18645455</id>
<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ |
| Intake point and Screen\\ | | | |
| | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | |
| Cartridge Seals \\ | | | |
| \\ | | | |
| \\ | \\ | \\ | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ |
| Filter Evacuate \\ | | | |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ |
| Direct Capture \\ | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ |
| | | | |
| Rotating Assembly \\ | | | |
| Rotation Mechanism \\ | | | |
| | | | |
| Cartridge Actuators \\ | | | |
| \\ | \\ | \\ | \\ |
| Cartridge Waste Collector | \\ | \\ | \\ |
| Waste Storage | | | |
| | | | |
| TRANSFER TO AM | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | |
| AM Selector Injection Loop \\ | | | |
| Clean Injection Loop \\ | | | |
| | | | |
| LRAUV Platform Interface \\ | | | |
| | | | |
Stop]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10944513</id>
<property name="body"><![CDATA[D-ESP get retrieved October 26, 2009 and re-deployed November 26, 2009.

&nbsp;Below, add to the list of 'to-dos' before the November deployment back on MARS:
# Complete integration of Data Aqcuisition subsystem
# Ground Fault subsystem
# Remote Host reset]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10911745</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">18645457</id>
<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ |
| Intake point and Screen \\ | | | |
| | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | |
| Cartridge Seals \\ | | | |
| \\ | | | |
| \\ | \\ | \\ | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ |
| Filter Evacuate \\ | | | |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ |
| Direct Capture \\ | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ |
| | | | |
| Rotating Assembly \\ | | | |
| Rotation Mechanism \\ | | | |
| | | | |
| Cartridge Actuators \\ | | | |
| \\ | \\ | \\ | \\ |
| Cartridge Waste Collector | \\ | \\ | \\ |
| Waste Storage | | | |
| | | | |
| TRANSFER TO AM | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | |
| AM Selector Injection Loop \\ | | | |
| Clean Injection Loop \\ | | | |
| Rotor Pass-Thru \\ | | | |
| LRAUV Platform Interface \\ | | | |
| | | | |
Stop]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">18579948</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10944514</id>
<property name="body"><![CDATA[D-ESP get retrieved October 27, 2009 and re-deployed November 26, 2009.

&nbsp;Below, add to the list of 'to-dos' before the November deployment back on MARS:
# Complete integration of Data Aqcuisition subsystem
# Ground Fault subsystem
# Remote Host reset]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10911746</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">18645453</id>
<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS |
| \\ | \\ | \\ | \\ |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | |
| Cartridge Seals \\ | | | |
| \\ | | | |
| \\ | \\ | \\ | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ |
| Filter Evacuate \\ | | | |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ |
| Direct Capture \\ | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ |
| | | | |
| Rotating Assembly \\ | | | |
| Rotation Mechanism \\ | | | |
| | | | |
| Cartridge Actuators \\ | | | |
| \\ | \\ | \\ | \\ |
| Cartridge Waste Collector | \\ | \\ | \\ |
| Waste Storage | | | |
| | | | |
| TRANSFER TO AM | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | |
| AM Selector Injection Loop \\ | | | |
| Clean Injection Loop \\ | | | |
| | | | |
| LRAUV Platform Interface \\ | | | |
| | | | |
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2019Feb08.pdf]
# [Engineering Timeline]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]

h2. Science]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 1 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 2 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 2 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  | 2 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 3 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 3 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 2 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ | 4 |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | | | | 2 |
| Rotation Mechanism \\ | | | | 2 |
| | | | | |
| Cartridge Actuators \\ | | | | |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | |
| Waste Storage | | | | |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | |
| AM Selector Injection Loop \\ | | | | |
| Clean Injection Loop \\ | | | | |
| Rotor Pass-Thru \\ | | | | |
| LRAUV Platform Interface \\ | | | | |
| | | | | |
Stop]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.

2: OEM components, or modified COTS.

3: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)

4: New prototype and designs, with known theory/physics, but unknown technologies and variables. (prototypes need to be designed and tested prior to deployment hardware design.)

5: New design needed, but no theory/physics are yet known that would enable the technology.

| G3 Function | Requirements | Technologies | COTS | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 1 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 2 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 2 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  | 2 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 3 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 3 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 2 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ | 4 |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | | | | 2 |
| Rotation Mechanism \\ | | | | 2 |
| | | | | |
| Cartridge Actuators \\ | | | | |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | |
| Waste Storage | | | | |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | |
| AM Selector Injection Loop \\ | | | | |
| Clean Injection Loop \\ | | | | |
| Rotor Pass-Thru \\ | | | | |
| LRAUV Platform Interface \\ | | | | |
| | | | | |
Stop]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [The MFB User's Manual]
# [MFB command help sheet|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1_7%2010_03_2008.doc]
# MFB chargers are Xenotronix HPX-30, and the batteries used are PowerSonic PS-12120 F2.

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/Fluidics_worksheet_04Dec08.pdf]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB BOM (2-28-2012)|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/BOM-REV%202012_02_28.xls]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [The MFB User's Manual]
# [MFB command help sheet|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1_7%2010_03_2008.doc]
# MFB chargers are Xenotronix HPX-30, and the batteries used are PowerSonic PS-12120 F2.

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/Fluidics_worksheet_04Dec08.pdf]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB BOM (2-28-2012)List|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/BOM-REV%202012_02_28.xls]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [The MFB User's Manual]
# [MFB command help sheet|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1_7%2010_03_2008.doc]
# MFB chargers are Xenotronix HPX-30, and the batteries used are PowerSonic PS-12120 F2.

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/Fluidics_worksheet_04Dec08.pdf]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/fluid%20worksheet%20MFB%2014-MAR-07.pdf]
# [Engineering Timeline]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]

h2. Science]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ | 4 |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | | | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
*  | * &nbsp;Worm drives
* Direct gear drives
* Geneva mechanism
*  | \\ | 2 \\ |
| | | | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ | 4 |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | | | | 2\\ |
| Rotation Mechanism \\ | | | | 2\\ |
| | | | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[h3. Administrative

(if asked to 'authenticate' in order to download anything, use 'shore/username')

# [The MFB User's Manual]
# [MFB command help sheet|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1_7%2010_03_2008.doc]
# MFB chargers are Xenotronix HPX-30, and the batteries used are PowerSonic PS-12120 F2.

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/Fluidics_worksheet_04Dec08.pdf]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB BOM (2-28-2012)|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/BOM-REV%202012_02_28.xls]
]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [The MFB User's Manual]
# [MFB command help sheet|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1_7%2010_03_2008.doc]
# MFB chargers are Xenotronix HPX-30, and the batteries used are PowerSonic PS-12120 F2.

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/Fluidics_worksheet_04Dec08.pdf]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB BOM (2-28-2012)|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/BOM-REV%202012_02_28.xls]

# \[try with Kevin

[this is the spreadsheet|^BOM-Rev 2012_02_28.xls|BOM]]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ | 4 |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| | | | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ | 4 |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments? | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller | \\ | 2 \\ |
| | | | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ | 4 |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | | | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments? | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller | \\ | 2 \\ |
| | | | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | | 5 |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ | 4 |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | | | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions\\
 or near infinite alignments? | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive | \\ | 2 \\ |
| | | | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note there we have yet to have made a batch of high-volume pucks,&nbsp;\\]]></property>
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<property name="body"><![CDATA[Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;]]></property>
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<property name="body"><![CDATA[h3. Deployment Update


h3. Machine Builds


h3. MFB





h3. Software





h3. DWSM


h5. &nbsp;


h3. GUI Development


h3. Other Items:]]></property>
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<property name="body"><![CDATA[h1. ESP Meeting


h4. &nbsp;Items:

* &nbsp;Chris P, Roman, Mike P meeting at 2:00pm today to finalize the BOM for the MFB
* March 14 looks good for field trip to Sandia in Livermore
* Jim will get Material Transfer Agreement for the Qiagen material;&nbsp; Scott Burrows may come visit March 6.
* We need to set up Confluence page to allow LRAUV access
* {color:#cc0000}Will come up with decision tree on technologies to use by Feb 28.&nbsp; Will then Review on March 1 when Chris can attend.{color}

h4. Puget Sound Deployment

* &nbsp;2 deployments, both using cell-phone and on piers.
** First will be late May to late June, while Vera is teaching a class at Friday Harbor.
** Second will be in August in Samish Bay (lat/long is 48.610416,-122.437445).
** NOAA has no operating funds and will need arrays, pucks, and reagents.
** deployment logistics still to be worked out.
** We will want to install HOBO's in their machine to watch for temp fluctuations
** {color:#cc0000}Must set-up site-visit dates.{color}

h4. Cawthron

* Chris and Kevan have a reagent list.&nbsp; Roman to provide what Puget Sound will need.&nbsp; This order and the dates needed will be given to Spyglass this week(?)
* &nbsp;Look into bonding our container shipment to speed through customs.

h4. 3G ESP

* &nbsp;Spoke at length with Doucette/Connel about their reagent needs in the Gen 3 instrument.&nbsp; Bead beating looks like a great thing for them.
* Right now, aqueous methanol extraction works and would require 3 reagents total:&nbsp; aq MeOH, primary Ab, PNA buffer.
* from 1 ml of aq MeOH lysate, pull 250ul for Ab labeling and/or 250ul for PNA labeling before sending to SPR.
* Work on Dissolved DA revolves around running filtered water through a resin to concentrate.&nbsp; Hope is that methanol would be the eluate and everything downstream would be same as above.&nbsp; form factor of resin column is not decided yet.&nbsp; Greg and Nick working on this right now. ]]></property>
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<property name="body"><![CDATA[h3. Deployments as they happened:

*{+}First network deployment{+}*

April 3&nbsp;&nbsp;  &nbsp;&nbsp;  Deploy Mack (M0)
April 21&nbsp;&nbsp;&nbsp; Recover Mack&nbsp;
\\

May 1&nbsp;&nbsp;&nbsp; Deploy Mack (M0)
May 12&nbsp;&nbsp;&nbsp; Mack craps out (syringe sticking)
May 15&nbsp;&nbsp;&nbsp; Recover Mack and can swap with Bruce
May 27&nbsp;&nbsp;&nbsp; Recover Bruce
May 28&nbsp;&nbsp;&nbsp; Deploy Mack and Neo (SC and M0)
June 30&nbsp;&nbsp;&nbsp; Recover Mack and Bruce&nbsp;

*{+}MB08 Deployment{+}*

October 8;&nbsp; Deploy Mack to Santa Cruz, Neo and Bruce at M0
October 27;&nbsp; recover all]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]]]></property>
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<property name="body"><![CDATA[h3. Deployments as they happened:

April 3&nbsp;&nbsp;  &nbsp;&nbsp;  Deploy Mack (M0)
April 21&nbsp;&nbsp;&nbsp; Recover Mack&nbsp;
\\

May 1&nbsp;&nbsp;&nbsp; Deploy Mack (M0)
May 12&nbsp;&nbsp;&nbsp; Mack craps out (syringe sticking)
May 15&nbsp;&nbsp;&nbsp; Recover Mack and can swap with Bruce
May 27&nbsp;&nbsp;&nbsp; Recover Bruce
May 28&nbsp;&nbsp;&nbsp; Deploy Mack and Neo (SC and M0)
June 30&nbsp;&nbsp;&nbsp; Recover Mack and Bruce&nbsp;]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2019Feb08.pdf]
# [Engineering Timeline]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]

h2. Science]]></property>
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<property name="body"><![CDATA[Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note that we have yet to make a full batch of high-volume snap pucks, but when we do, those will be labeled 1HV (top and bottom).]]></property>
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[G3 Process Diagrams|https://oceana.mbari.org/confluence/download/attachments/18579871/G3process.pptx]]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 21, 2008*

*11am-12*
Present: Jim, Doug, Chris S., Addie, Cheri, Kevin G.

LATEST Deployment Schedule is [HERE|ESPAPP:2008 Q1-Q2 Schedule (rev 4)].&nbsp;

h3. Tech Transfer


h6. Discussion Items:

* Update on Mack progress
** {color:#339999}Cheri noticed on Tuesday (19th) that the compression bolts are not gripping the motor shafts tightly enough.&nbsp; This stopped all preparation for the mock-mission run, and demanded a re-design of the valve/motor connection, which Doug helped brainstorm and propose a solution.&nbsp; 2mm balls are required for the fix, and, after calling every ball bearing place in 3 counties, we had to rely on MacMaster (delivered today).{color}

* &nbsp;Mike Parker contacted about piezoprinter problems (holding down membrane, cutting out disks) and is designing solutions.&nbsp; Also will be approached about a puck holder.

* New syringes.
** {color:#339999}Still not heard back from company{color}

* Screens and scintered frits
* &nbsp;
** {color:#339999}CE metalurgical will create a 'stamp' to label the frits.&nbsp; Cost is $300/tool.&nbsp; Will label at 1/2radius on one side of frit.{color}

* Puck Laser Etching
** {color:#339999}Mike put in SAF bottom holes, but got confirmation from El Camino on remaining pucks to not forget that again.&nbsp; Remaining pucks from first batch ready for etching.&nbsp; Then to send out lot3 for etching.&nbsp; Have spoken to Roman and Nilo about this.&nbsp;{color}

h3. MFB

Discussion Items:

&nbsp;After seasoning the tube, gels show that we are getting product produced (using calf thymus).&nbsp; Addie will begin work for the Moore year-end report.

h3. Software

* puck heating control
** {color:#339999}Brent has gotten calibration w/in 4degrees, but measuring puck temp is problematic.{color}
* Firmware 'lock-down'?
** Thermal boards and Dwarf boards look fine, but the failing home sensor in the hand seems to generate a cascade of failures.&nbsp; This will be fixed.(Brent)
** GG and Neo will have old firmware and old Ruby.&nbsp; Mack will use newer of each and these versions need to be kept separate.

h3. Sphere and 4K DWSMS

* Sphere update
** {color:#339999}No word or update from Wah Chang.{color}

* DWSM progress?
** {color:#339999}Doug believes he's found a pump that will push reliable, reproducible amounts of fluid.&nbsp; Ordering motor to run it, and now must test that it pushes the correct volumes of fluids with no back-flow.{color}
* Battery boxes?&nbsp; {color:#339999}Will order 1 box (~$2200; acct 701312.04; Scott){color}

ACTION:&nbsp; Have BATTERIES been ordered? (Jose)
ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)&nbsp;

h3. GUI Development

* Mission script GUI introduction

Kevin has placed new GUI on the server here.&nbsp; Rich Schramm available to do data parsing work; we want to utilize this by Sept deployment.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.]]></property>
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<property name="body"><![CDATA[# [2008 Q1-Q2 Schedule (rev 1)]
# [2008 Q1-Q2 Schedule (rev 2)]
# [2008 Q1-Q2 Schedule (rev 3)]
# [2008 Q1-Q2 Schedule (rev 4)]
# [Machinist build schedule (Feb 2007)]]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]
# [04Sep2008]
# [11Sep2008]
# [18Sep2008]
# [25Sep2008]
# [02Oct2008] (Pre-deployment discussions)
# [09Oct2008] (the day after deployment....)
# [16Oct2008]
# [23Oct2008]]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 21, 2008*

*11am-12*
Present: Jim, Doug, Chris S., Addie, Cheri, Kevin G.

LATEST Deployment Schedule is [HERE|ESPAPP:2008 Meeting Notes].&nbsp;

h3. Tech Transfer


h6. Discussion Items:

* Update on Mack progress
** {color:#339999}Cheri noticed on Tuesday (19th) that the compression bolts are not gripping the motor shafts tightly enough.&nbsp; This stopped all preparation for the mock-mission run, and demanded a re-design of the valve/motor connection, which Doug helped brainstorm and propose a solution.&nbsp; 2mm balls are required for the fix, and, after calling every ball bearing place in 3 counties, we had to rely on MacMaster (delivered today).{color}

* &nbsp;Mike Parker contacted about piezoprinter problems (holding down membrane, cutting out disks) and is designing solutions.&nbsp; Also will be approached about a puck holder.

* New syringes.
** {color:#339999}Still not heard back from company{color}

* Screens and scintered frits
* &nbsp;
** {color:#339999}CE metalurgical will create a 'stamp' to label the frits.&nbsp; Cost is $300/tool.&nbsp; Will label at 1/2radius on one side of frit.{color}

* Puck Laser Etching
** {color:#339999}Mike put in SAF bottom holes, but got confirmation from El Camino on remaining pucks to not forget that again.&nbsp; Remaining pucks from first batch ready for etching.&nbsp; Then to send out lot3 for etching.&nbsp; Have spoken to Roman and Nilo about this.&nbsp;{color}

h3. MFB

Discussion Items:

&nbsp;After seasoning the tube, gels show that we are getting product produced (using calf


h3. Software

* puck heating control
** {color:#339999}Brent has gotten calibration w/in 4degrees, but measuring puck temp is problematic.{color}
* Firmware 'lock-down'?
** Thermal boards and Dwarf boards look fine, but the failing home sensor in the hand seems to generate a cascade of failures.&nbsp; This will be fixed.(Brent)
** GG and Neo will have old firmware and old Ruby.&nbsp; Mack will use newer of each and these versions need to be kept separate.

h3. Sphere and 4K DWSMS

* Sphere update
** {color:#339999}No word or update from Wah Chang.{color}

* DWSM progress?
** {color:#339999}Doug believes he's found a pump that will push reliable, reproducible amounts of fluid.&nbsp; Ordering motor to run it, and now must test that it pushes the correct volumes of fluids with no back-flow.{color}
* Battery boxes?&nbsp; {color:#339999}Will order 1 box (~$2200; acct 701312.04; Scott){color}

ACTION:&nbsp; Have BATTERIES been ordered? (Jose)
ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)&nbsp;

h3. GUI Development

* Mission script GUI introduction

Kevin has placed new GUI on the server here.&nbsp; Rich Schramm available to do data parsing work; we want to utilize this by Sept deployment.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.]]></property>
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<property name="body"><![CDATA[| G3 Function | Requirements | Technologies | COTS |
| \\ | \\ | \\ | \\ |
| Isolation | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-batter | Direct lift solenoid valves \\
Custom body valves (thread into a SAE 4 port) \\
Size: less than c-battery, \\  \\
Axial flow thru valves \\
Turn or axial pull valves \\
Multi port valves \\
Automated actuators of above valves. \\
Multiple bank valves integrated on a chip | \\ |
| Filter | \\ | 25mm diameter surface filtering media \\
Similar area, but other geometry filters \\  \\
Filter integration in mount/seal/chip/cartridge \\ | \\ |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* Unaffected by saltwater
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can
*  | Piston pumps \\
Rotating piston (Similar to DWSM) \\
Syringes (with or without flow valves) \\
Gear pumps (low expectation) \\
Peristaltic&nbsp; (low expectation) \\
Progressive cavity (typically large frame) \\
Diaphragm \\  \\
Others? \\  \\ | \\ |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ |
| Sample purify | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ |
| Transfer to AM | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | \\ |
| \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ |
Stop]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]]]></property>
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<property name="body"><![CDATA[# [Science Meetings]
# [Engineering Meetings]
]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[| G3 Function | Requirements | Technologies | COTS |
| ISOLATION \\ | \\ | \\ | \\ |
| Ambient Sea/Flush selector valve \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | |
| Cartridge array valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | |
| Cartridge check valves \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | |
| Sea Pressure fittings \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  |
| Filter holder sealing\\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | |
| Filter selection valving\\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | |
| | | | |
| FILTER | \\ | \\ | |
| Filter Media \\ | \\ | 25mm diameter surface filtering media \\
Similar area, but other geometry filters \\  \\
Filter integration in mount/seal/chip/cartridge \\ | \\ |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* Unaffected by saltwater
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can
*  | Piston pumps \\
Rotating piston (Similar to DWSM) \\
Syringes (with or without flow valves) \\
Gear pumps (low expectation) \\
Peristaltic&nbsp; (low expectation) \\
Progressive cavity (typically large frame) \\
Diaphragm \\  \\
Others? \\  \\ | \\ |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ |
| Sample purify | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ |
| Transfer to AM | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | \\ |
| \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ |
Stop]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]
# [May 20]
# [May 27]
# June 3
# June 10
# [June 17]
# June 24 \-\- Scott led
# July 1 \-\- Doug led
# [July 8]
# Jul 15 \--Preparation for Methane cruise
# Jul 22 \--Methane cruise
# Jul 29 \--Methane cruise
# [Aug 5]
# [Aug 12]
# [Aug 19]
# [Aug 26]
# [Sep 2]
# [Sep 9] \--CANON cruise, Scholin in England
# [Sep 16]]]></property>
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<property name="body"><![CDATA[| G3 Function | Requirements | Technologies | COTS |
| ISOLATION \\ | \\ | \\ | \\ |
| Ambient Sea/Flush selector valve \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | \\ | \\ |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | |
| Cartridge array valves\\ | * &nbsp;Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | |
| Cartridge check valves\\ | * &nbsp;reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | |
| Sea Pressure fittings\\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  |
| | | | |
| FILTER | \\ | \\ | |
| Filter Media\\ | \\ | 25mm diameter surface filtering media \\
Similar area, but other geometry filters \\  \\
Filter integration in mount/seal/chip/cartridge \\ | \\ |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* Unaffected by saltwater
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can
*  | Piston pumps \\
Rotating piston (Similar to DWSM) \\
Syringes (with or without flow valves) \\
Gear pumps (low expectation) \\
Peristaltic&nbsp; (low expectation) \\
Progressive cavity (typically large frame) \\
Diaphragm \\  \\
Others? \\  \\ | \\ |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ |
| Sample purify | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ |
| Transfer to AM | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | \\ |
| \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ |
Stop]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound.

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deploymentMOE @ M0-\- w/PCR, ISUS.&nbsp; 72m water depth
{color:#33cc00}September 29{color} \-\- Bruce @ offshore (SC) with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; \-122.0455 36.895. 52m water depth.&nbsp; Weight measurements are [HERE|ESPAPP:Weight Calculations for BRUCE|mooring weights].
{color:#33ff00}September 28{color} \-\- Mack @ bight \--&nbsp; no ISUS. no PCR; Using RNALater as preservative.&nbsp; \-121.9241, 36.9329.&nbsp; 19m water depth]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound.

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deploymentMOE @ M0-\- w/PCR, ISUS.&nbsp; 72m water depth
Bruce @ offshore (SC)-\- with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; \-122.0455 36.895. 52m water depth.&nbsp; Weight measurements are HERE.
Mack @ bight \--&nbsp; no ISUS.&nbsp; Using RNALater as preservative.&nbsp; \-121.9241, 36.9329.&nbsp; 19m water depth]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound.

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deploymentMOE @ M0-\- w/PCR, ISUS.&nbsp; 72m water depth
Bruce @ offshore (SC)-\- with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; \-122.0455 36.895. 52m water depth&nbsp;
Mack @ bight \--&nbsp; no ISUS.&nbsp; Using RNALater as preservative.&nbsp; \-121.9241, 36.9329.&nbsp; 19m water depth]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound.

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\]]></property>
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<property name="body"><![CDATA[*Regarding Bruce's post can QC errors:*

Roman and I now believe that the camera seal did not go to the DA puck

rather than the other way 'round :-) If you look at the high-res image

shortDA08oct2909h100ml70s.tif

one can plainly see that the puck is bright and blurry, but the filter spots

are in focus.  Is it possible that the camera seal spring loaded seal mechanism

got stuck?  Note that, if this were to happen in the can, we probably would not

even notice it, as it would be already very dark in there anyway.
\\

If we don't think the mechanism got stuck, we should do some tests do determine

how far out of position the elevator would have to be to yield an image like the

one observed.   (spots in focus with puck body clearly visible)
\\

*Regarding Mack's hand being unable to pull the flush puck from its garage*:

The forearm was barely moving with high current levels when these errors occurred.

Recall the the current limit on the Forearm axis is set so high that an overcurrent cannot

occur unless the motor short circuits.  The upshot is that the forearm was stuck.

Could the ball bearing spring mechanism that holds the flushpuck in place be sticking

in the "up" position?


We've seen this before...
\\

@08:49:14.96@I2C::Servo::AbsMoveQuery[37:20->26]#0 to 2650
@08:49:15.68@I2C::Servo::AbsMoveReply[37:26->20] trajectoryErr with status:

@08:49:15.70@Slide::Error: Forearm trajectoryErr
@08:49:15.73@Retry #1 of 3
...


I just tried to manually remove the flush puck from its garage on Mack

and Bruce.&nbsp; Bruce had the normal detent.&nbsp; Mack's appeared to be stuck in its garage.&nbsp;

I did not remove it so others could compare.
\\]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound.

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deploymentMOE @ M0-\- w/PCR, ISUS.&nbsp; 72m water depth
Bruce @ offshore (SC)-\- with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; \-122.0455 36.895. 52m water depth.&nbsp; Weight measurements are [HERE|ESPAPP:Weight Calculations for BRUCE|mooring weights].
{color:#33ff00}September 28{color} \--Mack @ bight \--&nbsp; no ISUS.&nbsp; Using RNALater as preservative.&nbsp; \-121.9241, 36.9329.&nbsp; 19m water depth]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS |
| ISOLATION \\ | \\ | \\ | \\ |
| Ambient Sea/Flush selector valve \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | |
| Cartridge array valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | |
| Cartridge check valves \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | |
| Sea Pressure fittings \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | |
| | | | |
| FILTER | \\ | \\ | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ |
| Sample purify | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ |
| Transfer to AM | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | \\ |
| \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ |
Stop]]></property>
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<property name="body"><![CDATA[| G3 Function | Requirements | Technologies | COTS |
| ISOLATION \\ | \\ | \\ | \\ |
| Ambient Sea/Flush selector valve \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | |
| Cartridge array valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | |
| Cartridge check valves \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | |
| Sea Pressure fittings \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | |
| | | | |
| FILTER | \\ | \\ | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ |
| Sample purify | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ |
| Transfer to AM | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | \\ |
| \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ |
Stop]]></property>
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<property name="body"><![CDATA[Interesting idea about flush pucks being stuck.&nbsp; Chris and I gave them a good scrubbing before deployment....

Spoke with Mark Brown about our need for considerable Jose time; he said just talk to Jose who, if too overloaded, will go to Mark.&nbsp; I will try and see him tomorrow (Friday) ]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound.

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deploymentMOE @ M0-\- w/PCR, ISUS.&nbsp; 72m water depth
Bruce @ offshore (SC)-\- with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; \-122.0455 36.895. 52m water depth.&nbsp; Weight measurements are [HERE|ESPAPP:Weight Calculations for BRUCE|mooring weights].
Mack @ bight \--&nbsp; no ISUS.&nbsp; Using RNALater as preservative.&nbsp; \-121.9241, 36.9329.&nbsp; 19m water depth]]></property>
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<property name="body"><![CDATA[{gliffy:name=G3-Turbine- Functional Block Diagram|space=ESPAPP|page=ESP -- SURF Center Main Page|pageid=2162822|align=left|size=L}
h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[Triple Deployment Sept 28-Nov 3

Weight calcs as follows:
|| All in lbs \\ || || diff || ||
| Mooring wt (can & anchor) in air \\ | 1314 | | |
| Mooring wt w/anchor in water \\ | 1205 | 109 | |
| Can weight in air \\ | 754 | | |
| Anchor wt in air (1314-754) \\ | 560 | | |
| Anchor wt in water (560-119) \\ | 441 | | |
| Mooring wt (can & anchor) in water \\ | 297 \\ | | |
| Buoyancy of mooring (441-297) \\ | 144 | | |
\\]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS |
| ISOLATION \\ | \\ | \\ | \\ |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | |
| Cartridge array valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | |
| Cartridge Selection Valves \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | |
| Sea Pressure fittings \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | |
| | | | |
| FILTER | \\ | \\ | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ |
| Sample purify | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ |
| Transfer to AM | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | \\ |
| \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ |
Stop]]></property>
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<property name="body"><![CDATA[Present: Chris S., Scott, Kevin, Jim, Doug, Wayne, Addie

Absent: Cheri, Brent

h3. Deployment Update

* Thanks to all on an awesome deployment
* Post-can QC:
** Bruce has a leak, so images not looking good.&nbsp; South Carolina wants to do some tests; if we can do in 1 week great, otherwise should send their reagents back.&nbsp; Cheri back on Monday and will work on finding leak.
** All three instruments having Ruby issues (losing syringe/valve/hand/carousel positions, sign-inversions, or "I can't find myself" errors).&nbsp; Will meet with Brent about these problems.
** Chris & Scott will work on tracking down the bad puck Bruce had during the deployment to see if there's a smoking gun...

h3. Machine Builds

* harmonic drive has been running all week; working better, but Scott needs to check it more closely.&nbsp;

h3. MFB

* &nbsp;Addie: wil check with Jose about status of voltage regulator boards
* 64MB host boards (4) ordered; host ribbon cables ordered
* Lots of work for Jose that may require formal work request.&nbsp; Jim will check with Mark Brown
** measuring for wire harness; MBARI will build 2, rest will be sent out
** after these measurements, Jose/Scott will do schematic
** Jose will also be involved with serial connector to PCR builds and making 1 connector joining Grill to core or to stand-alone power supply.
* Jim will contact LLNL about January PCR module delivery
* NAMING CONVENTION:&nbsp; Grills will be sequentially numbered starting with MFB01.&nbsp; Subsequent will be MFB02, MFB03, MFB04, etc.

h3. Software

* &nbsp;If we decide to roll-out new Ruby code, it is better to do earlier than later as we'll need a stable platform by March.&nbsp; Must meet with Brent for debugging NEO results.
* See 2009 schedule below:

h3. DWSM


h6. +Sphere+

* &nbsp;Roughly 2 weeks machining left
** bottom is off lathe and in mill; finishing ports
** top is in lathe; found a void--worried there may be others.&nbsp; Waiting on X-ray quote from Tapemation.&nbsp; Doug to notify Wah Chang, who may be responsible for repair.
* will be using vulcanized assembled O-rings @ $15/each.
* Fasteners to be ordered--Ti vs. SS; still getting prices and lead times, but whether we go on Northern expedition or go on MARS will influence which we purchase
* bulkhead penetrations still to be made in-house;&nbsp; will talk to Scott about min-K connectors
* Where will sphere sit upon delivery? Will ask about back of Larry's space or storing in high-bay.

h6. +DWSM+

* Build has begun; currently waiting on Dean's valve parts
* much testing can be done with current dwarves; all boards for testing are available through Dick.

h3. GUI Development

* GUI is now parsing data.&nbsp; Kevin wants to store in Alfresco since this is accessible via the web to outsiders without having to give out MBARI accounts.

h3. Other Items:

* Bldg B lab will eventually need cleaning; Doug has his space along east wall; center will be where cores sit.&nbsp;

*{+}2009 deployment schedule looks like this :+*
* Winter/Spring \-\- series of DWSM/sphere test deployments.&nbsp; Last will be a Flyer deployment (5 days?), then several week break, then Northern Expedition in July.
* &nbsp;Spring \-\- series of S. California pier deployments; dates and lengths flexible, but likely 3 machines in three different cities for 1 month(?)
* End of 2009 \-\- MARS deployment
* &nbsp;Above could change if N. Expedition gets canceled due to budget issues.&nbsp; Will know more after Nov. 13 Packard Board mtg.]]></property>
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<property name="body"><![CDATA[Triple Deployment Sept 28-Nov 3

Weight calcs as follows:
|| All in lbs\\ || || diff || ||
| Mooring wt (can & anchor) in air\\ | 1314 | | |
| Mooring wt w/anchor in water\\ | 1205 | 119 | |
| Can weight in air \\ | 754 | | |
| Anchor wt in air (1314-754)\\ | 560 | | |
| Anchor wt in water (570-119)\\ | 441 | | |
| Mooring wt (can & anchor) in water\\ | 297 \\ | | |
| Buoyancy of mooring (441-297)\\ | 144 | | |
\\]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies | COTS |
| ISOLATION \\ | \\ | \\ | \\ |
| Intake Selector Valve\\
 \\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | |
| Cartridge array valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | |
| Cartridge check valves \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | |
| Sea Pressure fittings \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings | * Dibafit
* Upchurch
*  |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | |
| | | | |
| FILTER | \\ | \\ | |
| Filter Media \\ | * 25mm dia (effective) area
*  | \\ | \\ |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ |
| Lyse | * Up to 1mL of buffer + beads
* Sample particles on filter
*  | Bead Beating \\
Heating \\
Integrated heater/filter fit or holder \\
Grinding \\
Magnetic driven beating/grinding \\
Acoustic/Sonic \\
Automation of the above in closed volumes \\ | \\ |
| Sample purify | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | RNA and DNA extraction from one sample \\
Magnetic bead \\
Glass bead/fiber columns \\
Non-centrifuge wash processes. \\
Automated systems that perform the above. | \\ |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ |
| Transfer to AM | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | \\ |
| \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ |
Stop]]></property>
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<property name="body"><![CDATA[Present: Chris S., Scott, Kevin, Jim, Doug, Wayne, Addie

Absent: Cheri, Brent

h3. Deployment Update

* Thanks to all on an awesome deployment
* Post-can QC:
** Bruce has a leak, so images not looking good.&nbsp; South Carolina wants to do some tests; if we can do in 1 week great, otherwise should send their reagents back.&nbsp; Cheri back on Monday and will work on finding leak.
** All three instruments having Ruby issues (losing syringe/valve/hand/carousel positions, sign-inversions, or "I can't find myself" errors).&nbsp; Will meet with Brent about these problems.
** Chris & Scott will work on tracking down the bad puck Bruce had during the deployment to see if there's a smoking gun...

h3. Machine Builds

* harmonic drive has been running all week; working better, but Scott needs to check it more closely.&nbsp;

h3. MFB

* &nbsp;Addie: wil check with Jose about status of voltage regulator boards
* 64MB host boards (4) ordered; host ribbon cables ordered
* Lots of work for Jose that may require formal work request.&nbsp; Jim will check with Mark Brown
** measuring for wire harness; MBARI will build 2, rest will be sent out
** after these measurements, Jose/Scott will do schematic
** Jose will also be involved with serial connector to PCR builds and making 1 connector joining Grill to core or to stand-alone power supply.
* Jim will contact LLNL about January PCR module delivery
* NAMING CONVENTION:&nbsp; Grills will be sequentially numbered starting with MFB01.&nbsp; Subsequent will be MFB02, MFB03, MFB04, etc.

h3. Software

* &nbsp;If we decide to roll-out new Ruby code, it is better to do earlier than later as we'll need a stable platform by March.&nbsp; Must meet with Brent for debugging NEO results.
* See 2009 schedule below:

h3. DWSM


h6. +Sphere+

* &nbsp;Roughly 2 weeks machining left
** bottom is off lathe and in mill; finishing ports
** top is in lathe; found a void--worried there may be others.&nbsp; Waiting on X-ray quote from Tapemation.&nbsp; Doug to notify Wah Chang, who may be responsible for repair.
* will be using vulcanized assembled O-rings @ $15/each.
* Fasteners to be ordered--Ti vs. SS; still getting prices and lead times, but whether we go on Northern expedition or go on MARS will influence which we purchase
* bulkhead penetrations still to be made in-house;&nbsp; will talk to Scott about min-K connectors
* Where will sphere sit upon delivery? Will ask about back of Larry's space or storing in high-bay.

h6. +DWSM+

* Build has begun; currently waiting on Dean's valve parts
* much testing can be done with current dwarves; all boards for testing are available through Dick.

h3. GUI Development

* GUI is now parsing data.&nbsp; Kevin wants to store in Alfresco since this is accessible via the web to outsiders without having to give out MBARI accounts.

h3. Other Items:

* Bldg B lab will eventually need cleaning; Doug has his space along east wall; center will be where cores sit.&nbsp;

*{+}2009 deployment schedule looks like this :+*
* Winter/Spring \-\- series of DWSM/sphere test deployments.&nbsp; Last will be a Flyer deployment (5 days?), then several week break, then Northern Expedition in July.
* &nbsp;Spring \-\- series of S. California pier deployments; dates and lengths flexible, but likely 3 machines in three different cities for 1 month
* End of 2009 \-\- MARS deployment
* &nbsp;Above could change if N. Expedition gets canceled due to budget issues.&nbsp; Will know more after Nov. 13 Packard Board mtg.]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]]]></property>
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<property name="body"><![CDATA[Priority, What we need, (number).&nbsp;

Black \--> we do in house, {color:#0000ff}Blue \--> can be sent out (Mike decides){color}
* 1, Mushroom caps - 1003526-004 \-(20) {color:#ff0000}\- Mike has made (5) and will send the rest out for quote (1/31/08){color}
* -1, Bulkhead V. mounting brackets - P-200325-07 - (6)- {color:#ff0000}(02/04/08){color}
* -1, Plate Caps (2)- {color:#ff0000}\- (1/31/08){color}
* 1-Mike, {color:#0000ff}Waste Container - 1003526-001 - (2){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08) PO #0810307{color}
* 1-Mike, {color:#0000ff}Waste container supports - 1003526-003 - (6){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08) PO #0810307{color}
* 1-Mike, {color:#0000ff}Bag Hanger Assemblies - 1003523-01-02-03 - (5){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08) PO #0810307{color}

| {color:#009900}Bag Assembly Parts&nbsp;{color} | {color:#009900}For 5 Instruments{color} | {color:#009900}We currently have{color} | {color:#009900}We thus need (minimum){color} |
| -Hoops- | 10L&nbsp; 5mL&nbsp; 15sm \\ | 4L&nbsp; 1mL&nbsp; 2sm \\ | -6L&nbsp; 4mL&nbsp; 13sm- {color:#ff0000}(02/11/08){color} \\ |
| Crescent Closet Bar \\ | 7 | 3 | 4 |
| Bushing Assemb 4/instrument \\ | 20 | 14 | 6 |
* 2, Modem Battery cylinder - 10020051-01 - (1)
* 2, {color:#0000ff}Sample ports - 1002516 - (4){color}
* 2, spin can zinc down (3)
* 2, can-side CTD bracket (2)
* 2, {color:#0000ff}sample intake copper screen holder - 1002516-02 - (4){color}
* 2, bail locking plates (4)
* 2, adaptor plate for mooring (2)
* -3, CTV mount - 1002330-019 - (3)- {color:#ff0000}(2/04/08){color}
* -3, forearm motor shaft adaptor - 1002451-006 - (2)- {color:#ff0000}(02/05/08){color}
* -3, finger motor shaft adaptor - 1002451-006 short - (2)- {color:#ff0000}(02/05/08){color}
* 3, slot the encoder shafts (8)]]></property>
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<property name="body"><![CDATA[# [Jan 31]]]></property>
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<property name="body"><![CDATA[Priority, What we need, (number).&nbsp;

Black \--> we do in house, {color:#0000ff}Blue \--> can be sent out (Mike decides){color}
* 1, Mushroom caps - 1003526-004 \-(20) {color:#ff0000}\- Mike has made (5) and will send the rest out for quote (1/31/08){color}
* -1, Bulkhead V. mounting brackets - P-200325-07 - (6)- {color:#ff0000}(02/04/08){color}
* -1, Plate Caps (2)- {color:#ff0000}\- (1/31/08){color}
* 1-Mike, {color:#0000ff}Waste Container - 1003526-001 - (2){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08){color}
* 1-Mike, {color:#0000ff}Waste container supports - 1003526-003 - (6){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08){color}
* 1-Mike, {color:#0000ff}Bag Hanger Assemblies - 1003523-01-02-03 - (5){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08){color}

| {color:#009900}Bag Assembly Parts&nbsp;{color} | {color:#009900}For 5 Instruments{color} | {color:#009900}We currently have{color} | {color:#009900}We thus need (minimum){color} |
| Hoops | 10L&nbsp; 5mL&nbsp; 15sm \\ | 4L&nbsp; 1mL&nbsp; 2sm \\ | 6L&nbsp; 4mL&nbsp; 13sm \\ |
| Crescent Closet Bar \\ | 7 | 3 | 4 |
| Bushing Assemb 4/instrument \\ | 20 | 14 | 6 |
* 2, Modem Battery cylinder - 10020051-01 - (1)
* 2, {color:#0000ff}Sample ports - 1002516 - (4){color}
* 2, spin can zinc down (3)
* 2, can-side CTD bracket (2)
* 2, {color:#0000ff}sample intake copper screen holder - 1002516-02 - (4){color}
* 2, bail locking plates (4)
* 2, adaptor plate for mooring (2)
* -3, CTV mount - 1002330-019 - (3)- {color:#ff0000}(2/04/08){color}
* -3, forearm motor shaft adaptor - 1002451-006 - (2)- {color:#ff0000}(02/05/08){color}
* -3, finger motor shaft adaptor - 1002451-006 short - (2)- {color:#ff0000}(02/05/08){color}
* 3, slot the encoder shafts (8)]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<id name="id">3179019</id>
<property name="body"><![CDATA[# [2008 Q1-Q2 Schedule (rev 1)]
# [2008 Q1-Q2 Schedule (rev 2)]
# [Machinist build schedule (Feb 2007)]]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 7, 2008*

*11am-12*
Present: Jim, Doug, Scott, Brent, Cheri, Chris S., Kevin

Absent: Addie&nbsp;

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.
** {color:#339999}Brent wants to re-do some temperature calibrations with core placed inside box to remove air current effects.&nbsp; Will calibrate thermocouples this PM and get collection-side offsets tomorrow so science can start using on Monday the 11th.{color}
** {color:#339999}This PM Cheri will also calibrate Mack's hand{color}

* &nbsp; Mike Parker Machining list \-\- working quickly through it
** {color:#339999}Doug/Cheri worked on prototype of an adjustable temp sensor and will talk to Mike about it.&nbsp; Needs a priority.&nbsp; Will implement into Bruce, Mack will remain as is.{color}

* New syringes.
** {color:#339999}Still not heard back from company{color}

* Screens and scintered frits
** {color:#339999}Yesterday Scott sent plans to company for quote.{color}
** {color:#339999}We will order enough screens for 6 instruments.&nbsp; As soon as we have screen costs, we'll know how much money we have left and order scintered frits accordingly{color}

* Camera Discussion
** {color:#339999}Chris S. has found the 2x2 binning works well, so cameras will remain at f2.5 with \~2mm focus depth-of-field.{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

h3. MFB

Discussion Items:

ACTION:&nbsp; Addie to look at heating profile times to make sure we are not cooking our reaction. (Addie)&nbsp; {color:#ff0000}In progress{color}

h3. Software

* puck heating control
** {color:#339999}Brent needs one more day to get a better approximation on the collection side.&nbsp; Needs another puck--should be finished today.{color}
* Brent added code that reversed polarity of the motor encoders, since these new motor-mounts have encoder rotating opposite direction of originals.

+Action Items:+&nbsp;

ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment (Brent): {color:#ff0000}Low priority Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carousal and alignment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}

h3. Sphere and 4K DWSMS

* Sphere update
** {color:#339999}Wah Chang has changed their procedure, and will only make one part, have it checked, then cast the second article.&nbsp; If something wrong with the first one, we will be 2 months late and must reschedule all the late 2008 deployments.&nbsp; If all goes well, 2nd half will be cast in June.&nbsp; Can get both from Tapemation in August.&nbsp; Send to Port Hueneme for pressure testing and get back mid-Sept.{color}&nbsp;

* DWSM progress?
** {color:#339999}Aqualung up a running.&nbsp; It does everything except accurately measure volumes pumped.&nbsp; Finding correct pumps has been difficult.&nbsp; Doug has several backup ideas including going to a syringe/piston system.&nbsp; Stirring pump found to generate much heat when submerged in oil, as well as leach out lubricant/coating so several ideas floated to balance friction (and thus power consumption) and stirring capability.&nbsp; Maybe try lighter oil.{color}
* Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}

{color:#000000}ACTION:{color}&nbsp; Waiting for company to return yes/no on whether they can manufacture screens to mass instead of size. (Doug/Scott)&nbsp; {color:#0000ff}Finished{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price.&nbsp; Must order BATTERIES for deployment.
ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)&nbsp;

h3. GUI Development

* Mission script GUI introduction

Kevin to meet with Brent to discuss mission script GUI.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
\\ \\]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 7, 2008*

*11am-12*
Present: Jim,
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp;&nbsp;
** {color:#339999}Mack has been cold-tested and Brent is working on temp sensor testing.{color}
** {color:#339999}Bruce--all valves are in, hand mostly assembled, still to finish plumbing{color}
* Mike Parker Machining list \-\- working quickly through it
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; {color:#339999}N{color}
** {color:#339999}New hands to be ordered this summer.&nbsp; XX hand assemblies + 3 sets of fingers with new fulcrum positions to replace the existing 'new' fingers{color}
* New syringe cost.&nbsp;
** {color:#339999}Still not heard back from company{color}
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp;
** {color:#339999}Jose still forming the database.&nbsp; Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612,&nbsp; maybe a subaccount (.99 for CIP)).{color}

+Action Items+
\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

h3. MFB

Discussion Items:
* Getting excellent yields out of solid-phase-extraction--Good job Addie and Chris P\!\!
* Mixing column basically finished
* next week will make extract from seawater lysate and compare to bench-top
* in parallel, do dye tests with heater block.

ACTION:&nbsp; Hook up heater block and test diodes for fluorescence sensitivity. (Addie)&nbsp; {color:#ff0000}In progress{color}



h3. Software

* puck heating control
** now can send a temperature to puck and it gets there in 2-3 minutes with little overshoot
* Brent would like to pull calibration values out into a structure, since they are different on each instrument

+Action Items:+&nbsp;

ACTION:&nbsp; Finish by Feb 6 the temperature calibration model, incorporating Scott's prior work if possible. (Brent)
ACTION:&nbsp; make another temperature puck (Scott)
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment (Brent): {color:#ff0000}Low priority Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}

h3. Sphere and 4K DWSMS

* Screen drawings.&nbsp;

Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}
* DWSM progress?&nbsp;&nbsp; {color:#339999}Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.{color}

{color:#000000}ACTION:{color}&nbsp; Waiting for company to return yes/no on whether they can manufacture screens to mass instead of size. (Doug/Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price

h3. &nbsp;


h3. GUI Development

* Mission script GUI introduction

Kevin showed how to use the mission script GUI located here.
Bugs for this GUI can be reported here.&nbsp;
\\
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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# [Feb 2]
# [Feb 14]]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 7, 2008*

*11am-12*
Present: Jim, Doug, Scott, Brent, Cheri, Chris S., Kevin

Absent: Addie&nbsp;

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.
** {color:#339999}Brent wants to re-do some temperature calibrations with core placed inside box to remove air current effects.&nbsp; Will calibrate thermocouples this PM and get collection-side offsets tomorrow so science can start using on Monday the 11th.{color}
** {color:#339999}This PM Cheri will also calibrate Mack's hand{color}

* &nbsp; Mike Parker Machining list \-\- working quickly through it
** {color:#339999}Doug/Cheri worked on prototype of an adjustable temp sensor and will talk to Mike about it.&nbsp; Needs a priority.&nbsp; Will implement into Bruce, Mack will remain as is.{color}

* New syringes.
** {color:#339999}Still not heard back from company{color}

* Screens and scintered frits
** {color:#339999}Yesterday Scott sent plans to company for quote.{color}
** {color:#339999}We will order enough screens for 6 instruments.&nbsp; As soon as we have screen costs, we'll know how much money we have left and order scintered frits accordingly{color}

* Camera Discussion
** {color:#339999}Chris S. has found the 2x2 binning works well, so cameras will remain at f2.5 with \~2mm focus depth-of-field.{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

h3. MFB

Discussion Items:


ACTION:&nbsp; Addie to look at heating profile times to make sure we are not cooking our reaction. (Addie)&nbsp; {color:#ff0000}In progress{color}

h3. Software

* puck heating control
** {color:#339999}Brent needs one more day to get a better approximation on the collection side.&nbsp; Needs another puck--should be finished today.{color}
* Brent added code that reversed polarity of the motor encoders, since these new motor-mounts have encoder rotating opposite direction of originals.

+Action Items:+&nbsp;

ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment (Brent): {color:#ff0000}Low priority Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carousal and alignment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}

h3. Sphere and 4K DWSMS

* Sphere update
** {color:#339999}Wah Chang has changed their procedure, and will only make one part, have it checked, then cast the second article.&nbsp; If something wrong with the first one, we will be 2 months late and must reschedule all the late 2008 deployments.&nbsp; If all goes well, 2nd half will be cast in June.&nbsp; Can get both from Tapemation in August.&nbsp; Send to Port Hueneme for pressure testing and get back mid-Sept.{color}&nbsp;

* DWSM progress?
** {color:#339999}Aqualung up a running.&nbsp; It does everything except accurately measure volumes pumped.&nbsp; Finding correct pumps has been difficult.&nbsp; Doug has several backup ideas including going to a syringe/piston system.&nbsp; Stirring pump found to generate much heat when submerged in oil, as well as leach out lubricant/coating so several ideas floated to balance friction (and thus power consumption) and stirring capability.&nbsp; Maybe try lighter oil.{color}
* Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}

{color:#000000}ACTION:{color}&nbsp; Waiting for company to return yes/no on whether they can manufacture screens to mass instead of size. (Doug/Scott)&nbsp; {color:#0000ff}Finished{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price.&nbsp; Must order BATTERIES for deployment.
ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)&nbsp;

h3.  GUI Development

* Mission script GUI introduction

Kevin to meet with Brent to discuss mission script GUI.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 7, 2008*

*11am-12*
Present: Jim, Doug, Scott,

Absent: Addie&nbsp;

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp;&nbsp;
** {color:#339999}Mack has been cold-tested and Brent is working on temp sensor testing.{color}
** {color:#339999}Bruce--all valves are in, hand mostly assembled, still to finish plumbing{color}
* Mike Parker Machining list \-\- working quickly through it
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; {color:#339999}N{color}
** {color:#339999}New hands to be ordered this summer.&nbsp; XX hand assemblies + 3 sets of fingers with new fulcrum positions to replace the existing 'new' fingers{color}
* New syringe cost.&nbsp;
** {color:#339999}Still not heard back from company{color}
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp;
** {color:#339999}Jose still forming the database.&nbsp; Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612,&nbsp; maybe a subaccount (.99 for CIP)).{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

h3. MFB

Discussion Items:
* Getting excellent yields out of solid-phase-extraction--Good job Addie and Chris P\!\!
* Mixing column basically finished
* next week will make extract from seawater lysate and compare to bench-top
* in parallel, do dye tests with heater block.

ACTION:&nbsp; Hook up heater block and test diodes for fluorescence sensitivity. (Addie)&nbsp; {color:#ff0000}In progress{color}

h3. Software

* puck heating control
** now can send a temperature to puck and it gets there in 2-3 minutes with little overshoot
* Brent would like to pull calibration values out into a structure, since they are different on each instrument

+Action Items:+&nbsp;

ACTION:&nbsp; Finish by Feb 6 the temperature calibration model, incorporating Scott's prior work if possible. (Brent)
ACTION:&nbsp; make another temperature puck (Scott)
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment (Brent): {color:#ff0000}Low priority Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}

h3. Sphere and 4K DWSMS

* Screen drawings.&nbsp;

Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}
* DWSM progress?&nbsp;&nbsp; {color:#339999}Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.{color}

{color:#000000}ACTION:{color}&nbsp; Waiting for company to return yes/no on whether they can manufacture screens to mass instead of size. (Doug/Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price

h3. &nbsp;


h3. GUI Development

* Mission script GUI introduction

Kevin showed how to use the mission script GUI located here.
Bugs for this GUI can be reported here.&nbsp;
\\
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 14, 2008*

*11am-12*
Present: Jim, Doug, Chris S., Addie, Scott, Brent, Cheri, Rich S., Kevin G.

LATEST Deployment Schedule is [HERE|ESPAPP:2008 Q1-Q2 Schedule (rev 4)].&nbsp;

h3. Tech Transfer


h6. Discussion Items:

* Update on Mack progress
** {color:#339999}Have run into a hand homing issue.&nbsp; Replacement of everything, and movement of hand to another instrument has the issue following the hand.&nbsp; A new hand on Mack does not show this problem, but still unknown what is causing it.&nbsp; Otherwise, everything calibrated on Mack (hand, intake pressures, carousal).&nbsp;{color}
** {color:#339999}Dynamic control of puck temperatures is good, but still only able to hold within 4 degrees of setpoint.&nbsp; Most likely because temp sensor doesn't touch puck all that well, or this touching varies; thus final goal temperature is off.&nbsp; Regardless, Brent thinks we are much better than the GG and Neo runs last year.{color}
** {color:#339999}With the long weekend (Friday and Monday-Prez day) we will run non-stop mock missions through Mack (Flush, BAC, LARV,HAB, HAB-DA), before bagging on Tuesday and allowing science to run 'real' missions.&nbsp; Deployment schedule has changed (see above link).{color}

Chris' plan for the long weekend mock:
| Hi everyone - \\
\\
target temps are ideally: \\
\\
sh1 - 85C \\
DA - 70C \\
sh2 (laf, saf) - 30C \\
\\
having said that, we might we drop the actual setting on the esp a couple degrees to remain on the safer side of the line (hotter is worse).&nbsp; So Brent, use your judgement.&nbsp; I know a setting of e.g. 28 for sh2 sould be hard to hit when working in a warmish room, but worth a try? \\
\\
The outline of the simple&nbsp; mission for the faux run is given below.&nbsp; All sample vols should be 50 ml (sample for lysis and wcr).&nbsp; All reagent lines, including sample) will be filled with flush fluid.&nbsp; Exposures should be 160s 1x1, 40s 2x2, auto 2x2.&nbsp; Should we #-out the auto exp since there should be no light, or just let it burn till time-out for kicks? \\
\\
\\
\# before starting run prime all reagent lines and make sure to purge intake so the sample line is primed too. \\
\\
romanFlush&nbsp; #not sure this syntax is correct - Ro pls verify \\
bac \\
larv \\
hab \\
habda \\
da \\
\\
\#end \\
\\
this should be 22 pucks \-\- do you want to put them in a single stack or spread around? \\
\\ |
* &nbsp;Mike Parker contacted about piezoprinter problems (holding down membrane, cutting out disks) and is designing solutions.&nbsp; Also will be approached about a puck holder.

* New syringes.
** {color:#339999}Still not heard back from company{color}

* Screens and scintered frits
** {color:#339999}Will order 400 10um frits with frit packing tool. total cost $4300.00.&nbsp;{color} {color:#0000ff}Order placed 2-14-08{color}{color:#339999}.&nbsp; Here is the{color} {color:#339999}[{color:#339999}order{color}|frit order]{color} {color:#339999}and the{color} {color:#339999}[{color:#339999}quote{color}|Frit quote]{color}{color:#339999}.{color}
** {color:#339999}We will order enough screens for 6 instruments.&nbsp; (who is doing this?){color}

* Puck Laser Etching
** {color:#339999}first half of pucks have returned from the etching, and SH1 tops and HV puck tops are mislabled.&nbsp; Will investigate sending these back, as well as sending out the 2nd batch of lot2 pucks.&nbsp; The first 'new' batch (lot3) has arrived from El Camino, Mike P is inspecting.&nbsp; Has found they forgot to put hole in SAF bottoms.&nbsp; Will return to get that done.&nbsp; These pucks will go straight to etching before we&nbsp; get them.{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose still working to assemble a more accurate list of electronics/machine for a more accurate cost estimate

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

h3. MFB

Discussion Items:

&nbsp;Decided&nbsp; to run thermal cycler all weekend with just water and bleach, to see if extra 'seasoning' of the tubing will lessen its inhibition of the PCR reaction.&nbsp; Upon return next week, will run sample to test PCR effectivness.

ACTION:&nbsp; Addie to look at heating profile times to make sure we are not cooking our reaction. (Addie)&nbsp; {color:#0000ff}Finished{color}

h3. Software

* puck heating control
** {color:#339999}Brent has gotten calibration w/in 4degrees, but measuring puck temp is problematic.{color}
* Firmware 'lock-down'?
** Thermal boards and Dwarf boards look fine, but the failing home sensor in the hand seems to generate a cascade of failures.&nbsp; This will be fixed.(Brent)
** GG and Neo will have old firmware and old Ruby.&nbsp; Mack will use newer of each and these versions need to be kept separate.

h3. Sphere and 4K DWSMS

* Sphere update
** {color:#339999}No word or update from Wah Chang.{color}

* DWSM progress?
** {color:#339999}Doug believes he's found a pump that will push reliable, reproducible amounts of fluid.&nbsp; Ordering motor to run it, and now must test that it pushes the correct volumes of fluids with no back-flow.{color}
* Battery boxes?&nbsp; {color:#339999}Will order 1 box (~$2200; acct 701312.04; Scott){color}

ACTION:&nbsp; Have BATTERIES been ordered? (Jose)
ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)&nbsp;

h3. GUI Development

* Mission script GUI introduction

Kevin has placed new GUI on the server here.&nbsp; Rich Schramm available to do data parsing work; we want to utilize this by Sept deployment.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
\\
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 14, 2008*

*11am-12*
Present: Jim, Doug, Chris S., Addie, Scott, Brent, Cheri, Rich S., Kevin G.

LATEST Deployment Schedule is [HERE|ESPAPP:2008 Q1-Q2 Schedule (rev 4)].&nbsp;

h3. Tech Transfer


h6. Discussion Items:

* Update on Mack progress
** {color:#339999}Have run into a hand homing issue.&nbsp; Replacement of everything, and movement of hand to another instrument has the issue following the hand.&nbsp; A new hand on Mack does not show this problem, but still unknown what is causing it.&nbsp; Otherwise, everything calibrated on Mack (hand, intake pressures, carousal).&nbsp;{color}
** {color:#339999}Dynamic control of puck temperatures is good, but still only able to hold within 4 degrees of setpoint.&nbsp; Most likely because temp sensor doesn't touch puck all that well, or this touching varies; thus final goal temperature is off.&nbsp; Regardless, Brent thinks we are much better than the GG and Neo runs last year.{color}
** {color:#339999}With the long weekend (Friday and Monday-Prez day) we will run non-stop mock missions through Mack (Flush, BAC, LARV,HAB, HAB-DA), before bagging on Tuesday and allowing science to run 'real' missions.&nbsp; Deployment schedule has changed (see above link).{color}

Chris' plan for the long weekend mock:
| Hi everyone - \\
\\
target temps are ideally: \\
\\
sh1 - 85C \\
DA - 70C \\
sh2 (laf, saf) - 30C \\
\\
having said that, we might we drop the actual setting on the esp a couple degrees to remain on the safer side of the line (hotter is worse).&nbsp; So Brent, use your judgement.&nbsp; I know a setting of e.g. 28 for sh2 sould be hard to hit when working in a warmish room, but worth a try? \\
\\
The outline of the simple&nbsp; mission for the faux run is given below.&nbsp; All sample vols should be 50 ml (sample for lysis and wcr).&nbsp; All reagent lines, including sample) will be filled with flush fluid.&nbsp; Exposures should be 160s 1x1, 40s 2x2, auto 2x2.&nbsp; Should we #-out the auto exp since there should be no light, or just let it burn till time-out for kicks? \\
\\
\\
\# before starting run prime all reagent lines and make sure to purge intake so the sample line is primed too. \\
\\
romanFlush&nbsp; #not sure this syntax is correct - Ro pls verify \\
bac \\
larv \\
hab \\
habda \\
da \\
\\
\#end \\
\\
this should be 22 pucks \-\- do you want to put them in a single stack or spread around? \\
\\ |
* &nbsp;Mike Parker contacted about piezoprinter problems (holding down membrane, cutting out disks) and is designing solutions.&nbsp; Also will be approached about a puck holder.

* New syringes.
** {color:#339999}Still not heard back from company{color}

* Screens and scintered frits
** {color:#339999}Will order 400 10um frits with frit packing tool. total cost $4300.00.&nbsp;{color} {color:#0000ff}Order placed 2-14-08{color}{color:#339999}.&nbsp; Here is the{color} {color:#339999}order{color} {color:}and the{color} {color:#339999}quote{color}{color:}.{color}
** {color:#339999}We will order enough screens for 6 instruments.&nbsp; (who is doing this?){color}

* Puck Laser Etching
** {color:#339999}first half of pucks have returned from the etching, and SH1 tops and HV puck tops are mislabled.&nbsp; Will investigate sending these back, as well as sending out the 2nd batch of lot2 pucks.&nbsp; The first 'new' batch (lot3) has arrived from El Camino, Mike P is inspecting.&nbsp; Has found they forgot to put hole in SAF bottoms.&nbsp; Will return to get that done.&nbsp; These pucks will go straight to etching before we&nbsp; get them.{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose still working to assemble a more accurate list of electronics/machine for a more accurate cost estimate

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

h3. MFB

Discussion Items:

&nbsp;Decided&nbsp; to run thermal cycler all weekend with just water and bleach, to see if extra 'seasoning' of the tubing will lessen its inhibition of the PCR reaction.&nbsp; Upon return next week, will run sample to test PCR effectivness.

ACTION:&nbsp; Addie to look at heating profile times to make sure we are not cooking our reaction. (Addie)&nbsp; {color:#0000ff}Finished{color}

h3. Software

* puck heating control
** {color:#339999}Brent has gotten calibration w/in 4degrees, but measuring puck temp is problematic.{color}
* Firmware 'lock-down'?
** Thermal boards and Dwarf boards look fine, but the failing home sensor in the hand seems to generate a cascade of failures.&nbsp; This will be fixed.(Brent)
** GG and Neo will have old firmware and old Ruby.&nbsp; Mack will use newer of each and these versions need to be kept separate.

h3. Sphere and 4K DWSMS

* Sphere update
** {color:#339999}No word or update from Wah Chang.{color}

* DWSM progress?
** {color:#339999}Doug believes he's found a pump that will push reliable, reproducible amounts of fluid.&nbsp; Ordering motor to run it, and now must test that it pushes the correct volumes of fluids with no back-flow.{color}
* Battery boxes?&nbsp; {color:#339999}Will order 1 box (~$2200; acct 701312.04; Scott){color}

ACTION:&nbsp; Have BATTERIES been ordered? (Jose)
ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)&nbsp;

h3. GUI Development

* Mission script GUI introduction

Kevin has placed new GUI on the server here.&nbsp; Rich Schramm available to do data parsing work; we want to utilize this by Sept deployment.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
\\
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 14, 2008*

*11am-12*
Present: Jim, Doug, Chris S., Addie, Scott, Brent, Cheri, Rich S., Kevin G.

LATEST Deployment Schedule is [HERE|ESPAPP:2008 Q1-Q2 Schedule (rev 4)].&nbsp;

h3. Tech Transfer


h6. Discussion Items:

* Update on Mack progress
** {color:#339999}Have run into a hand homing issue.&nbsp; Replacement of everything, and movement of hand to another instrument has the issue following the hand.&nbsp; A new hand on Mack does not show this problem, but still unknown what is causing it.&nbsp; Otherwise, everything calibrated on Mack (hand, intake pressures, carousal).&nbsp;{color}
** {color:#339999}Dynamic control of puck temperatures is good, but still only able to hold within 4 degrees of setpoint.&nbsp; Most likely because temp sensor doesn't touch puck all that well, or this touching varies; thus final goal temperature is off.&nbsp; Regardless, Brent thinks we are much better than the GG and Neo runs last year.{color}
** {color:#339999}With the long weekend (Friday and Monday-Prez day) we will run non-stop mock missions through Mack (Flush, BAC, LARV,HAB, HAB-DA), before bagging on Tuesday and allowing science to run 'real' missions.&nbsp; Deployment schedule has changed (see above link).{color}

Chris' plan for the long weekend mock:
| Hi everyone - \\
\\
target temps are ideally: \\
\\
sh1 - 85C \\
DA - 70C \\
sh2 (laf, saf) - 30C \\
\\
having said that, we might we drop the actual setting on the esp a couple degrees to remain on the safer side of the line (hotter is worse).&nbsp; So Brent, use your judgement.&nbsp; I know a setting of e.g. 28 for sh2 sould be hard to hit when working in a warmish room, but worth a try? \\
\\
The outline of the simple&nbsp; mission for the faux run is given below.&nbsp; All sample vols should be 50 ml (sample for lysis and wcr).&nbsp; All reagent lines, including sample) will be filled with flush fluid.&nbsp; Exposures should be 160s 1x1, 40s 2x2, auto 2x2.&nbsp; Should we #-out the auto exp since there should be no light, or just let it burn till time-out for kicks? \\
\\
\\
\# before starting run prime all reagent lines and make sure to purge intake so the sample line is primed too. \\
\\
romanFlush&nbsp; #not sure this syntax is correct - Ro pls verify \\
bac \\
larv \\
hab \\
habda \\
da \\
\\
\#end \\
\\
this should be 22 pucks \-\- do you want to put them in a single stack or spread around? \\
\\ |
* &nbsp;Mike Parker contacted about piezoprinter problems (holding down membrane, cutting out disks) and is designing solutions.&nbsp; Also will be approached about a puck holder.

* New syringes.
** {color:#339999}Still not heard back from company{color}

* Screens and scintered frits
** {color:#339999}Will order 400 10um frits with frit packing tool. total cost $4300.00.&nbsp;{color} {color:#0000ff}Order placed 2-14-08{color}{color:#339999}.&nbsp; Here is the order and the quote.{color}
** {color:#339999}We will order enough screens for 6 instruments.&nbsp; (who is doing this?){color}

* Puck Laser Etching
** {color:#339999}first half of pucks have returned from the etching, and SH1 tops and HV puck tops are mislabled.&nbsp; Will investigate sending these back, as well as sending out the 2nd batch of lot2 pucks.&nbsp; The first 'new' batch (lot3) has arrived from El Camino, Mike P is inspecting.&nbsp; Has found they forgot to put hole in SAF bottoms.&nbsp; Will return to get that done.&nbsp; These pucks will go straight to etching before we&nbsp; get them.{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose still working to assemble a more accurate list of electronics/machine for a more accurate cost estimate

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

h3. MFB

Discussion Items:

&nbsp;Decided&nbsp; to run thermal cycler all weekend with just water and bleach, to see if extra 'seasoning' of the tubing will lessen its inhibition of the PCR reaction.&nbsp; Upon return next week, will run sample to test PCR effectivness.

ACTION:&nbsp; Addie to look at heating profile times to make sure we are not cooking our reaction. (Addie)&nbsp; {color:#0000ff}Finished{color}

h3. Software

* puck heating control
** {color:#339999}Brent has gotten calibration w/in 4degrees, but measuring puck temp is problematic.{color}
* Firmware 'lock-down'?
** Thermal boards and Dwarf boards look fine, but the failing home sensor in the hand seems to generate a cascade of failures.&nbsp; This will be fixed.(Brent)
** GG and Neo will have old firmware and old Ruby.&nbsp; Mack will use newer of each and these versions need to be kept separate.

h3. Sphere and 4K DWSMS

* Sphere update
** {color:#339999}No word or update from Wah Chang.{color}

* DWSM progress?
** {color:#339999}Doug believes he's found a pump that will push reliable, reproducible amounts of fluid.&nbsp; Ordering motor to run it, and now must test that it pushes the correct volumes of fluids with no back-flow.{color}
* Battery boxes?&nbsp; {color:#339999}Will order 1 box (~$2200; acct 701312.04; Scott){color}

ACTION:&nbsp; Have BATTERIES been ordered? (Jose)
ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)&nbsp;

h3. GUI Development

* Mission script GUI introduction

Kevin has placed new GUI on the server here.&nbsp; Rich Schramm available to do data parsing work; we want to utilize this by Sept deployment.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
\\
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 14, 2008*

*11am-12*
Present: Jim, Doug, Chris S., Addie, Scott, Brent, Cheri, Rich S., Kevin G.

LATEST Deployment Schedule is [HERE|ESPAPP:2008 Q1-Q2 Schedule (rev 4)].&nbsp;

h3. Tech Transfer


h6. Discussion Items:

* Update on Mack progress
** {color:#339999}Have run into a hand homing issue.&nbsp; Replacement of everything, and movement of hand to another instrument has the issue following the hand.&nbsp; A new hand on Mack does not show this problem, but still unknown what is causing it.&nbsp; Otherwise, everything calibrated on Mack (hand, intake pressures, carousal).&nbsp;{color}
** {color:#339999}Dynamic control of puck temperatures is good, but still only able to hold within 4 degrees of setpoint.&nbsp; Most likely because temp sensor doesn't touch puck all that well, or this touching varies; thus final goal temperature is off.&nbsp; Regardless, Brent thinks we are much better than the GG and Neo runs last year.{color}
** {color:#339999}With the long weekend (Friday and Monday-Prez day) we will run non-stop mock missions through Mack (Flush, BAC, LARV,HAB, HAB-DA), before bagging on Tuesday and allowing science to run 'real' missions.&nbsp; Deployment schedule has changed (see above link).{color}

Chris' plan for the long weekend mock:
| Hi everyone - \\
\\
target temps are ideally: \\
\\
sh1 - 85C \\
DA - 70C \\
sh2 (laf, saf) - 30C \\
\\
having said that, we might we drop the actual setting on the esp a couple degrees to remain on the safer side of the line (hotter is worse).&nbsp; So Brent, use your judgement.&nbsp; I know a setting of e.g. 28 for sh2 sould be hard to hit when working in a warmish room, but worth a try? \\
\\
The outline of the simple&nbsp; mission for the faux run is given below.&nbsp; All sample vols should be 50 ml (sample for lysis and wcr).&nbsp; All reagent lines, including sample) will be filled with flush fluid.&nbsp; Exposures should be 160s 1x1, 40s 2x2, auto 2x2.&nbsp; Should we #-out the auto exp since there should be no light, or just let it burn till time-out for kicks? \\
\\
\\
\# before starting run prime all reagent lines and make sure to purge intake so the sample line is primed too. \\
\\
romanFlush&nbsp; #not sure this syntax is correct - Ro pls verify \\
bac \\
larv \\
hab \\
habda \\
da \\
\\
\#end \\
\\
this should be 22 pucks \-\- do you want to put them in a single stack or spread around? \\
\\ |
* &nbsp;Mike Parker contacted about piezoprinter problems (holding down membrane, cutting out disks) and is designing solutions.&nbsp; Also will be approached about a puck holder.

* New syringes.
** {color:#339999}Still not heard back from company{color}

* Screens and scintered frits
** {color:#339999}Will order 400 10um frits with frit packing tool. total cost $4300.00.{color}
** {color:#339999}We will order enough screens for 6 instruments.&nbsp; (who is doing this?){color}

* Puck Laser Etching
** {color:#339999}first half of pucks have returned from the etching, and SH1 tops and HV puck tops are mislabled.&nbsp; Will investigate sending these back, as well as sending out the 2nd batch of lot2 pucks.&nbsp; The first 'new' batch (lot3) has arrived from El Camino, Mike P is inspecting.&nbsp; Has found they forgot to put hole in SAF bottoms.&nbsp; Will return to get that done.&nbsp; These pucks will go straight to etching before we&nbsp; get them.{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose still working to assemble a more accurate list of electronics/machine for a more accurate cost estimate

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

h3. MFB

Discussion Items:

&nbsp;Decided&nbsp; to run thermal cycler all weekend with just water and bleach, to see if extra 'seasoning' of the tubing will lessen its inhibition of the PCR reaction.&nbsp; Upon return next week, will run sample to test PCR effectivness.

ACTION:&nbsp; Addie to look at heating profile times to make sure we are not cooking our reaction. (Addie)&nbsp; {color:#0000ff}Finished{color}

h3. Software

* puck heating control
** {color:#339999}Brent has gotten calibration w/in 4degrees, but measuring puck temp is problematic.{color}
* Firmware 'lock-down'?
** Thermal boards and Dwarf boards look fine, but the failing home sensor in the hand seems to generate a cascade of failures.&nbsp; This will be fixed.(Brent)
** GG and Neo will have old firmware and old Ruby.&nbsp; Mack will use newer of each and these versions need to be kept separate.

h3. Sphere and 4K DWSMS

* Sphere update
** {color:#339999}No word or update from Wah Chang.{color}

* DWSM progress?
** {color:#339999}Doug believes he's found a pump that will push reliable, reproducible amounts of fluid.&nbsp; Ordering motor to run it, and now must test that it pushes the correct volumes of fluids with no back-flow.{color}
* Battery boxes?&nbsp; {color:#339999}Will order 1 box (~$2200; acct 701312.04; Scott){color}

ACTION:&nbsp; Have BATTERIES been ordered? (Jose)
ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)&nbsp;

h3. GUI Development

* Mission script GUI introduction

Kevin has placed new GUI on the server here.&nbsp; Rich Schramm available to do data parsing work; we want to utilize this by Sept deployment.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
\\
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 14, 2008*

*11am-12*
Present: Jim, Doug, Chris S., Addie, Scott, Brent, Cheri, Rich S., Kevin G.

LATEST Deployment Schedule is HERE.&nbsp;

h3. Tech Transfer


h6. Discussion Items:

* Update on Mack progress
** {color:#339999}Have run into a hand homing issue.&nbsp; Replacement of everything, and movement of hand to another instrument has the issue following the hand.&nbsp; A new hand on Mack does not show this problem, but still unknown what is causing it.&nbsp; Otherwise, everything calibrated on Mack (hand, intake pressures, carousal).&nbsp;{color}
** {color:#339999}Dynamic control of puck temperatures is good, but still only able to hold within 4 degrees of setpoint.&nbsp; Most likely because temp sensor doesn't touch puck all that well, or this touching varies; thus final goal temperature is off.&nbsp; Regardless, Brent thinks we are much better than the GG and Neo runs last year.{color}
** {color:#339999}With the long weekend (Friday and Monday-Prez day) we will run non-stop mock missions through Mack (Flush, BAC, LARV,HAB, HAB-DA), before bagging on Tuesday and allowing science to run 'real' missions.&nbsp; Deployment schedule has changed (see above link).{color}

Chris' plan for the long weekend mock:
| Hi everyone -\\
 \\
 target temps are ideally:\\
 \\
 sh1 - 85C \\
 DA - 70C \\
 sh2 (laf, saf) - 30C\\
 \\
 having said that, we might we drop the actual setting on the esp a couple degrees to remain on the safer side of the line (hotter is worse).&nbsp; So Brent, use your judgement.&nbsp; I know a setting of e.g. 28 for sh2 sould be hard to hit when working in a warmish room, but worth a try?\\
 \\
 The outline of the simple&nbsp; mission for the faux run is given below.&nbsp; All sample vols should be 50 ml (sample for lysis and wcr).&nbsp; All reagent lines, including sample) will be filled with flush fluid.&nbsp; Exposures should be 160s 1x1, 40s 2x2, auto 2x2.&nbsp; Should we #-out the auto exp since there should be no light, or just let it burn till time-out for kicks?\\
 \\
 \\
 \# before starting run prime all reagent lines and make sure to purge intake so the sample line is primed too.\\
 \\
 romanFlush&nbsp; #not sure this syntax is correct - Ro pls verify \\
 bac \\
 larv \\
 hab \\
 habda \\
 da\\
 \\
 \#end\\
 \\
 this should be 22 pucks \-\- do you want to put them in a single stack or spread around?\\
 \\ |
* &nbsp;Mike Parker contacted about piezoprinter problems (holding down membrane, cutting out disks) and is designing solutions.&nbsp; Also will be approached about a puck holder.

* New syringes.
** {color:#339999}Still not heard back from company{color}

* Screens and scintered frits
** {color:#339999}Will order 400 10um frits with frit packing tool. total cost $4300.00.{color}
** {color:#339999}We will order enough screens for 6 instruments.&nbsp; (who is doing this?){color}

* Puck Laser Etching
** {color:#339999}first half of pucks have returned from the etching, and SH1 tops and HV puck tops are mislabled.&nbsp; Will investigate sending these back, as well as sending out the 2nd batch of lot2 pucks.&nbsp; The first 'new' batch (lot3) has arrived from El Camino, Mike P is inspecting.&nbsp; Has found they forgot to put hole in SAF bottoms.&nbsp; Will return to get that done.&nbsp; These pucks will go straight to etching before we&nbsp; get them.{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose still working to assemble a more accurate list of electronics/machine for a more accurate cost estimate


ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

h3. MFB

Discussion Items:

&nbsp;Decided&nbsp; to run thermal cycler all weekend with just water and bleach, to see if extra 'seasoning' of the tubing will lessen its inhibition of the PCR reaction.&nbsp; Upon return next week, will run sample to test PCR effectivness.


ACTION:&nbsp; Addie to look at heating profile times to make sure we are not cooking our reaction. (Addie)&nbsp; {color:#0000ff}Finished{color}

h3. Software

* puck heating control
** {color:#339999}Brent has gotten calibration w/in 4degrees, but measuring puck temp is problematic.{color}
* Firmware 'lock-down'?
** Thermal boards and Dwarf boards look fine, but the failing home sensor in the hand seems to generate a cascade of failures.&nbsp; This will be fixed.(Brent)
** GG and Neo will have old firmware and old Ruby.&nbsp; Mack will use newer of each and these versions need to be kept separate.


h3. Sphere and 4K DWSMS

* Sphere update
** {color:#339999}No word or update from Wah Chang.{color}

* DWSM progress?
** {color:#339999}Doug believes he's found a pump that will push reliable, reproducible amounts of fluid.&nbsp; Ordering motor to run it, and now must test that it pushes the correct volumes of fluids with no back-flow.{color}
* Battery boxes?&nbsp; {color:#339999}Will order 1 box (~$2200; acct 701312.04; Scott){color}

ACTION:&nbsp; Have BATTERIES been ordered? (Jose)
ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)&nbsp;

h3. GUI Development

* Mission script GUI introduction

Kevin has placed new GUI on the server here.&nbsp; Rich Schramm available to do data parsing work; we want to utilize this by Sept deployment.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
\\
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<property name="body"><![CDATA[h1. ESP 'Science' Mtg


h4. Frackers

# Found that RNA quality is good enough to run microarrays; RIN numbers look good, but still unsure if 'bad' numbers would result in poor microarray results.&nbsp; Unclear what the future is with these results.
# Current extraction testing has been on 16s gene; must test functional genes and chris P getting p/p for rbcl, AOAa, and Roseobacter.&nbsp; Hope to have two finished this week.&nbsp; If these work, Chris has multitude of questions to move forward.&nbsp; Looks like enzymatic lysis will not work for RNA; works great for DNA, but too slow for RNA, allowing RNAses in to destroy RNA before complete lysis.
# Elif has finished standard curves for pier deployment and is now crunching then numbers.]]></property>
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<property name="body"><![CDATA[# [2008 Q1-Q2 Schedule (rev 1)]
# [2008 Q1-Q2 Schedule (rev 2)]
# [2008 Q1-Q2 Schedule (rev 3)]
# [Machinist build schedule (Feb 2007)]]]></property>
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<id name="id">3179112</id>
<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 14, 2008*

*11am-12*
Present:


LATEST Deployment Schedule is HERE.&nbsp;

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.
** {color:#339999}Brent wants to re-do some temperature calibrations with core placed inside box to remove air current effects.&nbsp; Will calibrate thermocouples this PM and get collection-side offsets tomorrow so science can start using on Monday the 11th.{color}
** {color:#339999}This PM Cheri will also calibrate Mack's hand{color}

* &nbsp; Mike Parker Machining list \-\- working quickly through it
** {color:#339999}Doug/Cheri worked on prototype of an adjustable temp sensor and will talk to Mike about it.&nbsp; Needs a priority.&nbsp; Will implement into Bruce, Mack will remain as is.{color}

* New syringes.
** {color:#339999}Still not heard back from company{color}

* Screens and scintered frits
** {color:#339999}Yesterday Scott sent plans to company for quote.{color}
** {color:#339999}We will order enough screens for 6 instruments.&nbsp; As soon as we have screen costs, we'll know how much money we have left and order scintered frits accordingly{color}

* Camera Discussion
** {color:#339999}Chris S. has found the 2x2 binning works well, so cameras will remain at f2.5 with \~2mm focus depth-of-field.{color}

+Action Items+
\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

h3. MFB

Discussion Items:

ACTION:&nbsp; Addie to look at heating profile times to make sure we are not cooking our reaction. (Addie)&nbsp; {color:#0000ff}Finished{color}

h3. Software

* puck heating control
** {color:#339999}Brent needs one more day to get a better approximation on the collection side.&nbsp; Needs another puck--should be finished today.{color}
* Brent added code that reversed polarity of the motor encoders, since these new motor-mounts have encoder rotating opposite direction of originals.

+Action Items:+&nbsp;

ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment (Brent): {color:#ff0000}Low priority Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carousal and alignment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}

h3. Sphere and 4K DWSMS

* Sphere update
** {color:#339999}Wah Chang has changed their procedure, and will only make one part, have it checked, then cast the second article.&nbsp; If something wrong with the first one, we will be 2 months late and must reschedule all the late 2008 deployments.&nbsp; If all goes well, 2nd half will be cast in June.&nbsp; Can get both from Tapemation in August.&nbsp; Send to Port Hueneme for pressure testing and get back mid-Sept.{color}&nbsp;

* DWSM progress?
** {color:#339999}Aqualung up a running.&nbsp; It does everything except accurately measure volumes pumped.&nbsp; Finding correct pumps has been difficult.&nbsp; Doug has several backup ideas including going to a syringe/piston system.&nbsp; Stirring pump found to generate much heat when submerged in oil, as well as leach out lubricant/coating so several ideas floated to balance friction (and thus power consumption) and stirring capability.&nbsp; Maybe try lighter oil.{color}
* Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}


ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price.&nbsp; Must order BATTERIES for deployment.
ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)&nbsp;

h3. GUI Development

* Mission script GUI introduction

Kevin to meet with Brent to discuss mission script GUI.
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
\\
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<property name="body"><![CDATA[Instrument Level
|| || Control Loops&nbsp; || || Inputs \\ || Outputs || || || || || ||
| 1 \\ | Sampling Pump \\ | | | | | | | | |
| 2 | Spool Valve Actuator \\ | | | | | | | | |
| 3 | Cylinder Rotate \\ | | | | | | | | |
| 4 | Cartridge Actuator Alignment \\ | | | | | | | | |
| 5 | Cartridge Actuator 1 \\ | | | | | | | | |
| 6 | Cartridge Actuator 2 | | | | | | | | |
| 7 | Cartridge Actuator 3 | | | | | | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | | | | | | |
| 9 | Cartridge Reagent Valve \\ | | | | | | | | |
| 10 | A/M Clamp \\ | | | | | | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | | | | | | |
| 12 | A/M Hand-off Syringe \\ | | | | | | | | |
| \\ | \\ | | | | | | | | |
| | | | | | | | | | |

|| || Discrete Actions || || \\ || Outputs || || || || || ||
| 1 \\ | Intake Select 1 \\ | | | | | | | | |
| 2 | Intake Select 2 \\ | | | | | | | | |
| 3 | Bulkhead valve (intake) \\ | | | | | | | | |
| 4 | Bulkhead valve (exhaust) | | | | | | | | |
| 5 | -Cartridge Valve Actuator 1- \\ | | | | | | | | |
| 6 | Cylinder latch \\ | | | | | | | | |
| 7 | A/M Valve 1 \\ | | | | | | | | |
| 8 | A/M Valve 2 \\ | | | | | | | | |
| 9 | A/M Valve 3 | | | | | | | | |
| 10 | A/M Valve 4 | | | | | | | | |
| 11 | A/M Clamp \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |
\\

Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
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Instrument Level
|| || Control Loops&nbsp; || || Inputs \\ || Outputs || || || || || ||
| 1 \\ | Sampling Pump \\ | | | | | | | | |
| 2 | Spool Valve Selector \\ | | | | | | | | |
| 3 | Cylinder Rotate \\ | | | | | | | | |
| 4 | Cartridge Actuator Alignment \\ | | | | | | | | |
| 5 | Cartridge Actuator 1 \\ | | | | | | | | |
| 6 | Cartridge Actuator 2 | | | | | | | | |
| 7 | Cartridge Actuator 3 | | | | | | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | | | | | | |
| 9 | Cartridge Reagent Valve \\ | | | | | | | | |
| 10 | A/M Clamp \\ | | | | | | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | | | | | | |
| 12 | A/M Hand-off Syringe \\ | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |

|| || Discrete Actions || || \\ || Outputs || || || || || ||
| 1 \\ | Intake Select 1 \\ | | | | | | | | |
| 2 | Intake Select 2 \\ | | | | | | | | |
| 3 | Bulkhead valve (intake) \\ | | | | | | | | |
| 4 | Bulkhead valve (exhaust) | | | | | | | | |
| 5 | Cartridge Valve Actuator 1 \\ | | | | | | | | |
| 6 | Cylinder latch \\ | | | | | | | | |
| 7 | A/M Valve 1 \\ | | | | | | | | |
| 8 | A/M Valve 2 \\ | | | | | | | | |
| 9 | A/M Valve 3 | | | | | | | | |
| 10 | A/M Valve 4 | | | | | | | | |
| 11 | A/M Clamp \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |
\\

Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
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<property name="body"><![CDATA[Instrument Level
|| || Control Loops&nbsp; || || Inputs \\ || Outputs || || || || || ||
| 1 \\ | Sampling Pump \\ | | | | | | | | |
| 2 | Spool Valve Selector \\ | | | | | | | | |
| 3 | Cylinder Rotate \\ | | | | | | | | |
| 4 | Cartridge Actuator Alignment \\ | | | | | | | | |
| 5 | Cartridge Actuator 1 \\ | | | | | | | | |
| 6 | Cartridge Actuator 2 | | | | | | | | |
| 7 | Cartridge Actuator 3 | | | | | | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | | | | | | |
| 9 | Cartridge Reagent Valve \\ | | | | | | | | |
| 10 | A/M Clamp \\ | | | | | | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | | | | | | |
| 12 | A/M Hand-off Syringe \\ | | | | | | | | |
| 13\\ | Cartridge Valve Actuator\\ | | | | | | | | |
| | | | | | | | | | |

|| || Discrete Actions || || \\ || Outputs || || || || || ||
| 1 \\ | Intake Select 1 \\ | | | | | | | | |
| 2 | Intake Select 2 \\ | | | | | | | | |
| 3 | Bulkhead valve (intake) \\ | | | | | | | | |
| 4 | Bulkhead valve (exhaust) | | | | | | | | |
| 5 | -Cartridge Valve Actuator 1- \\ | | | | | | | | |
| 6 | Cylinder latch \\ | | | | | | | | |
| 7 | A/M Valve 1 \\ | | | | | | | | |
| 8 | A/M Valve 2 \\ | | | | | | | | |
| 9 | A/M Valve 3 | | | | | | | | |
| 10 | A/M Valve 4 | | | | | | | | |
| 11 | A/M Clamp \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |
\\

Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
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<property name="body"><![CDATA[Instrument Level
|| || Control Loops&nbsp; || || Inputs \\ || Outputs || || || || || ||
| 1 \\ | Sampling Pump \\ | | | | | | | | |
| 2 | Spool Valve Actuator \\ | | | | | | | | |
| 3 | Cylinder Rotate \\ | | | | | | | | |
| 4 | Cartridge Actuator Alignment \\ | | | | | | | | |
| 5 | Cartridge Actuator 1 \\ | | | | | | | | |
| 6 | Cartridge Actuator 2 | | | | | | | | |
| 7 | Cartridge Actuator 3 | | | | | | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | | | | | | |
| 9 | Cartridge Reagent Valve \\ | | | | | | | | |
| 10 | A/M Clamp \\ | | | | | | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | | | | | | |
| 12 | A/M Hand-off Syringe \\ | | | | | | | | |
| 13 \\ | Cylinder Align/Lock \\ | | | | | | | | |
| | | | | | | | | | |

|| || Discrete Actions || || \\ || Outputs || || || || || ||
| 1 \\ | Intake Select 1 \\ | | | | | | | | |
| 2 | Intake Select 2 \\ | | | | | | | | |
| 3 | Bulkhead valve (intake) \\ | | | | | | | | |
| 4 | Bulkhead valve (exhaust) | | | | | | | | |
| 5 | -Cartridge Valve Actuator 1- \\ | | | | | | | | |
| 6 | -Cylinder latch- \\ | | | | | | | | |
| 7 | A/M Valve 1 \\ | | | | | | | | |
| 8 | A/M Valve 2 \\ | | | | | | | | |
| 9 | A/M Valve 3 | | | | | | | | |
| 10 | A/M Valve 4 | | | | | | | | |
| 11 | A/M Clamp \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |
\\

Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
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<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically (colors are same deployment)+

{color:#ff00ff}April 6--Bruce at M0 for surface deployment (Zephyr){color}

April 15--Mack in Sphere (dive #1) for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in Sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

{color:#ff00ff}April 29--Recover Bruce at M0 (Zephyr){color}

May 1--Mack in Sphere (dive #3) connected to DWSM; incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

{color:#0033cc}May 14--Deploy NEO w/PCR, surface deployment (Zephyr){color}

May 27--First Drifter dive; used weighted cable (Zephyr)

June 5-9 \-\- Western Flyer Trip.&nbsp; D-ESP, Drifter, and CTD casts. {color:#cc0000}{*}MOVIES{*}{color}:  D-ESP launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/DESP%20deployment%20(full%20quality).dv].  Drifter launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/Drifter.dv].

{color:#0033cc}June 11 \-\- Recover NEO.&nbsp; (Zephyr){color}\\

+FALL Network Deployment+

Proposed locations are here: [http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&msid=113879459163411006053.000471828af997bd7d89c&t=h&z=12]

September 24 \-\- Deploy Moe w/PCR at M0.&nbsp; Deployed Mack at Santa Cruz.&nbsp; {color:#66cc00}Deployed Bruce in the bight.&nbsp; (Zephyr)&nbsp; Lost communications with Bruce that day.{color}

{color:#66cc00}September 28 \-\- Recover (dead) Bruce.&nbsp; Comms box had water in it, but radio worked.&nbsp; EM cable had 2 broken wires. (Zephyr){color}

September 30 \-\- Deploy D-ESP on MARS (Lobos).&nbsp; Hand issue at first, but 'fixed' itself.&nbsp; Worked until Oct. 7 when wrong puck was loaded and water introduced into core, frying puck heater.&nbsp; We turned off and first recovery day (Oct 13) is weathered out.&nbsp; It still awaits recovery.

{color:#66cc00}October 14 \-\- Re-deploy Bruce.&nbsp; New comms box, re-terminated EM cable.&nbsp; Working well after deployment.{color} ]]></property>
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<property name="body"><![CDATA[h2. Overview

h2. Notes

The printer used by [~scholin] is a custom printer. It can not output GAL files. It does put out a text file that I'm trying to parse and work with. A copy of the file is checked into [SVN|http://kahuna.shore.mbari.org/viewvc.cgi/esp/trunk/esp-imaging/src/test/resources/imaging/2_22_08comptest_2008-02-25_142348_Run.txt?view=markup].

h3. Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:
{noformat}
SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK
{noformat}

SpotX and SpotY are coordinates in micrometers starting in the upper left hand corner of the paper. The _0, 0_ point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out

h3. References
# Old ESP Matlab toolbox at [http://moonjelly/cgi-bin/cvsweb.cgi/ESP/matlab/]
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<property name="body"><![CDATA[h2. Overview

h2. Notes

The printer used by [~scholin] is a custom printer. It can not output GAL files. It does put out a text file that I'm trying to parse and work with. A copy of the file is checked into [SVN|http://kahuna.shore.mbari.org/viewvc.cgi/esp/trunk/esp-imaging/src/test/resources/imaging/2_22_08comptest_2008-02-25_142348_Run.txt?view=markup].

h3. Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:
{noformat}
SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK
{noformat}

SpotX and SpotY are coordinates in micrometers starting in the upper left hand corner of the paper. The _0, 0_ point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out

h3. Image Analysis

Using ImageJ, it's possible to locate the spots using _Plugins -> Filters -> MultiThresholder_ (Select Maximum Entropy in the Dialog)

{gallery}

h3. References
# Old ESP Matlab toolbox at [http://moonjelly/cgi-bin/cvsweb.cgi/ESP/matlab/]
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<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically (colors are same deployment)+

{color:#ff00ff}April 6--Bruce at M0 for surface deployment (Zephyr){color}

April 15--Mack in Sphere (dive #1) for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in Sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

{color:#ff00ff}April 29--Recover Bruce at M0 (Zephyr){color}

May 1--Mack in Sphere (dive #3) connected to DWSM; incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

{color:#0033cc}May 14--Deploy NEO w/PCR, surface deployment (Zephyr){color}

May 27--First Drifter dive; used weighted cable (Zephyr)

June 5-9 \-\- Western Flyer Trip.&nbsp; D-ESP, Drifter, and CTD casts. {color:#cc0000}{*}MOVIES{*}{color}:  D-ESP launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/DESP%20deployment%20(full%20quality).dv].  Drifter launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/Drifter.dv].

{color:#0033cc}June 11 \-\- Recover NEO.&nbsp; (Zephyr){color}\\

+FALL Network Deployment+

Proposed locations are here: [http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&msid=113879459163411006053.000471828af997bd7d89c&t=h&z=12]

September 24 \-\- Deploy Moe w/PCR at M0.&nbsp; Deployed Mack at Santa Cruz.&nbsp; Deployed Bruce in the bight.&nbsp; (Zephyr)&nbsp; Lost communications with Bruce that day.

September 28 \-\- Recover (dead) Bruce.&nbsp; Comms box had water in it, but radio worked.&nbsp; EM cable had 2 broken wires. (Zephyr)

September 30 \-\- Deploy D-ESP on MARS (Lobos).&nbsp; Hand issue at first, but 'fixed' itself.]]></property>
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<property name="body"><![CDATA[h2. Overview

h2. Notes

The printer used by [~scholin] is a custom printer. It can not output GAL files. It does put out a text file that I'm trying to parse and work with. A copy of the file is checked into [SVN|http://kahuna.shore.mbari.org/viewvc.cgi/esp/trunk/esp-imaging/src/test/resources/imaging/2_22_08comptest_2008-02-25_142348_Run.txt?view=markup].

h3. Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:
{noformat}
SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK
{noformat}

SpotX and SpotY are coordinates in micrometers starting in the upper left hand corner of the paper. The _0, 0_ point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out

h3. Image Analysis

Using ImageJ, it's possible to locate the spots using _Plugins -> Filters -> MultiThresholder_ (Select _Maximum Entropy_ in the Dialog)

{gallery}

h3. References
# Old ESP Matlab toolbox at [http://moonjelly/cgi-bin/cvsweb.cgi/ESP/matlab/]
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<property name="body"><![CDATA[Priority, What we need, (number).&nbsp;

Black \--> we do in house, {color:#0000ff}Blue \--> can be sent out (Mike decides){color}
* 1, Mushroom caps - 1003526-004 \-(20) {color:#ff0000}\- Mike has made (5) and will send the rest out for quote (1/31/08){color}
* -1, Bulkhead V. mounting brackets - P-200325-07 - (6)- {color:#ff0000}(02/04/08){color}
* -1, Plate Caps (2)- {color:#ff0000}\- (1/31/08){color}
* 1-Mike, {color:#0000ff}Waste Container - 1003526-001 - (2){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08) PO #0810307 -{color} {color:#000000}Rcvd 3/3/08{color}
* 1-Mike, {color:#0000ff}Waste container supports - 1003526-003 - (6){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08) PO #0810307 -{color} {color:#000000}Rcvd 3/3/08{color}
* 1-Mike, {color:#0000ff}Bag Hanger Assemblies - 1003523-01-02-03 - (5){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08) PO #0810307 -{color} {color:#000000}Rcvd 3/3/08{color}

| {color:#009900}Bag Assembly Parts&nbsp;{color} | {color:#009900}For 5 Instruments{color} | {color:#009900}We currently have{color} | {color:#009900}We thus need (minimum){color} |
| -Hoops- | 10L&nbsp; 5mL&nbsp; 15sm \\ | 4L&nbsp; 1mL&nbsp; 2sm \\ | -6L&nbsp; 4mL&nbsp; 13sm- {color:#ff0000}(02/11/08){color} \\ |
| Crescent Closet Bar \\ | 7 | 3 | 4 {color:#ff0000}Rcvd 3/3/08{color} |
| Bushing Assemb 4/instrument \\ | 20 | 14 | -6- {color:#ff0000}None Needed{color} |
* 2, Modem Battery cylinder - 10020051-01 - (1)
* 2, {color:#0000ff}Sample ports - 1002516 - (4){color} {color:#ff0000}(2/19/08){color}
* 2, spin can zinc down (3)
* 2, can-side CTD bracket (2)
* 2, {color:#0000ff}sample intake copper screen holder - 1002516-02 - (4){color}
* 2, bail locking plates (4)
* 2, adaptor plate for mooring (2)
* {color:#ff0000}2, Shaft Adapter for Maxon-to-Valve - Replacement for ShaftLoks \-&nbsp;(qty. 30?){color}
* -3, CTV mount - 1002330-019 - (3)- {color:#ff0000}(2/04/08){color}
* -3, forearm motor shaft adaptor - 1002451-006 - (2)- {color:#ff0000}(02/05/08){color}
* -3, finger motor shaft adaptor - 1002451-006 short - (2)- {color:#ff0000}(02/05/08){color}
* -3, slot the encoder shafts (8)- {color:#ff0000}(02/11/08){color}
* {color:#ff0000}3 Parker Pucker Un-Stuckers - Solids and Prints ready (02/12/08){color}\\]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision
# [25Jun2009]
# 02Jul2009 - no meeting; 4th of July break
# [09Jul2009]
# [16Jul2009]
# [23Jul2009]
# 30Jul2009 - Scott ran mtg; proposal preparation
# [06Aug2009]
# 13Aug2009 - cancelled; proposal/grant preparations
# [20Aug2009]
# 27Aug2009 - Jim Vacation; Scott in charge
# 03Sep2009 - Jim Vacation; Scott in charge
# [10Sep2009]
# [01Oct2009]
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<property name="body"><![CDATA[!G3 Control Layout1.png|thumbnail!
&nbsp;
Instrument Level
|| || Control Loops&nbsp; || || Inputs \\ || Outputs || Torque/Force \\ || Speed range \\ || Accuracy \\ || Precision \\ || ||
| 1 \\ | Sampling Pump \\ | | | | | | | | |
| 2 | Spool Valve Actuator \\ | | | | | | | | |
| 3 | Cylinder Rotate \\ | | | | | | | | |
| 4 | Cartridge Actuator Alignment \\ | | | | | | | | |
| 5 | Cartridge Actuator 1 \\ | | | | | | | | |
| 6 | Cartridge Actuator 2 | | | | | | | | |
| 7 | Cartridge Actuator 3 | | | | | | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | | | | | | |
| 9 | Cartridge Reagent Valve \\ | | | | | | | | |
| 10 | A/M Clamp \\ | | | | | | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | | | | | | |
| 12 | A/M Hand-off Syringe \\ | | | | | | | | |
| 13 \\ | Cylinder Align/Lock \\ | | | | | | | | |
| | | | | | | | | | |

|| || Discrete Actions || || \\ || Outputs || || || || || ||
| 1 \\ | Intake Select 1 \\ | | | | | | | | |
| 2 | Intake Select 2 \\ | | | | | | | | |
| 3 | Bulkhead valve (intake) \\ | | | | | | | | |
| 4 | Bulkhead valve (exhaust) | | | | | | | | |
| 5 | -Cartridge Valve Actuator 1- \\ | | | | | | | | |
| 6 | -Cylinder latch- \\ | | | | | | | | |
| 7 | A/M Valve 1 \\ | | | | | | | | |
| 8 | A/M Valve 2 \\ | | | | | | | | |
| 9 | A/M Valve 3 | | | | | | | | |
| 10 | A/M Valve 4 | | | | | | | | |
| 11 | A/M Clamp \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |

|| || Raw Input \\ || || Range \\ || \\ || || || || || ||
| 1 \\ | ABS Pressure intake \\ | \\ | 0-500psia \\ | | | | | | |
| 2 | ABS Pressure exhaust \\ | \\ | 0-500psia \\ | | | | | | |
| 3 | intake/exhaust pressure differential \\ | | | | | | | | |
| 4 | \\ | | | | | | | | |
| 5 | \\ | | | | | | | | |
| 6 | \\ | | | | | | | | |
| 7 | \\ | | | | | | | | |
| 8 | \\ | | | | | | | | |
| 9 | \\ | | | | | | | | |
| 10 | \\ | | | | | | | | |
| 11 | \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |
Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
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<property name="body"><![CDATA[!G3 Control Layout1.png|thumbnail!
&nbsp;
Instrument Level
|| || Control Loops&nbsp; || || Inputs \\ || Outputs || Torque/Force \\ || Speed range \\ || Accuracy \\ || Precision \\ || ||
| 1 \\ | Sampling Pump \\ | | | | | | | | |
| 2 | Spool Valve Actuator \\ | | | | | | | | |
| 3 | Cylinder Rotate \\ | | | | | | | | |
| 4 | Cartridge Actuator Alignment \\ | | | | | | | | |
| 5 | Cartridge Actuator 1 \\ | | | | | | | | |
| 6 | Cartridge Actuator 2 | | | | | | | | |
| 7 | Cartridge Actuator 3 | | | | | | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | | | | | | |
| 9 | Cartridge Reagent Valve \\ | | | | | | | | |
| 10 | A/M Clamp \\ | | | | | | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | | | | | | |
| 12 | A/M Hand-off Syringe \\ | | | | | | | | |
| 13 \\ | Cylinder Align/Lock \\ | | | | | | | | |
| | | | | | | | | | |

|| || Discrete Actions || || \\ || Outputs || || || || || ||
| 1 \\ | Intake Select 1 \\ | | | | | | | | |
| 2 | Intake Select 2 \\ | | | | | | | | |
| 3 | Bulkhead valve (intake) \\ | | | | | | | | |
| 4 | Bulkhead valve (exhaust) | | | | | | | | |
| 5 | -Cartridge Valve Actuator 1- \\ | | | | | | | | |
| 6 | -Cylinder latch- \\ | | | | | | | | |
| 7 | A/M Valve 1 \\ | | | | | | | | |
| 8 | A/M Valve 2 \\ | | | | | | | | |
| 9 | A/M Valve 3 | | | | | | | | |
| 10 | A/M Valve 4 | | | | | | | | |
| 11 | A/M Clamp \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |

|| || Raw Input\\ || || \\ || Outputs || || || || || ||
| 1 \\ | \\ | \\ | \\ | | | | | | |
| 2 | \\ | \\ | \\ | | | | | | |
| 3 | \\ | | | | | | | | |
| 4 | \\ | | | | | | | | |
| 5 | \\ | | | | | | | | |
| 6 | \\ | | | | | | | | |
| 7 | \\ | | | | | | | | |
| 8 | \\ | | | | | | | | |
| 9 | \\ | | | | | | | | |
| 10 | \\ | | | | | | | | |
| 11 | \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |
Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
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<property name="body"><![CDATA[!G3 Control Layout1.png|thumbnail!
&nbsp;
Instrument Level
|| || Control Loops&nbsp; || || Inputs \\ || Outputs || Torque/Force \\ || Speed range \\ || Accuracy \\ || Precision \\ || ||
| 1 \\ | Sampling Pump \\ | | | | | | | | |
| 2 | Spool Valve Actuator \\ | | | | | | | | |
| 3 | Cylinder Rotate \\ | | | | | | | | |
| 4 | Cartridge Actuator Alignment \\ | | | | | | | | |
| 5 | Cartridge Actuator 1 \\ | | | | | | | | |
| 6 | Cartridge Actuator 2 | | | | | | | | |
| 7 | Cartridge Actuator 3 | | | | | | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | | | | | | |
| 9 | Cartridge Reagent Valve \\ | | | | | | | | |
| 10 | A/M Clamp \\ | | | | | | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | | | | | | |
| 12 | A/M Hand-off Syringe \\ | | | | | | | | |
| 13 \\ | Cylinder Align/Lock \\ | | | | | | | | |
| | | | | | | | | | |

|| || Discrete Actions || || \\ || Outputs || || || || || ||
| 1 \\ | Intake Select 1 \\ | | | | | | | | |
| 2 | Intake Select 2 \\ | | | | | | | | |
| 3 | Bulkhead valve (intake) \\ | | | | | | | | |
| 4 | Bulkhead valve (exhaust) | | | | | | | | |
| 5 | -Cartridge Valve Actuator 1- \\ | | | | | | | | |
| 6 | -Cylinder latch- \\ | | | | | | | | |
| 7 | A/M Valve 1 \\ | | | | | | | | |
| 8 | A/M Valve 2 \\ | | | | | | | | |
| 9 | A/M Valve 3 | | | | | | | | |
| 10 | A/M Valve 4 | | | | | | | | |
| 11 | A/M Clamp \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |
\\

Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
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<property name="body"><![CDATA[!G3 Control Layout1.png|thumbnail!
&nbsp;
Instrument Level
|| || Control Loops&nbsp; || || Inputs \\ || Outputs || || || || || ||
| 1 \\ | Sampling Pump \\ | | | | | | | | |
| 2 | Spool Valve Actuator \\ | | | | | | | | |
| 3 | Cylinder Rotate \\ | | | | | | | | |
| 4 | Cartridge Actuator Alignment \\ | | | | | | | | |
| 5 | Cartridge Actuator 1 \\ | | | | | | | | |
| 6 | Cartridge Actuator 2 | | | | | | | | |
| 7 | Cartridge Actuator 3 | | | | | | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | | | | | | |
| 9 | Cartridge Reagent Valve \\ | | | | | | | | |
| 10 | A/M Clamp \\ | | | | | | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | | | | | | |
| 12 | A/M Hand-off Syringe \\ | | | | | | | | |
| 13 \\ | Cylinder Align/Lock \\ | | | | | | | | |
| | | | | | | | | | |

|| || Discrete Actions || || \\ || Outputs || || || || || ||
| 1 \\ | Intake Select 1 \\ | | | | | | | | |
| 2 | Intake Select 2 \\ | | | | | | | | |
| 3 | Bulkhead valve (intake) \\ | | | | | | | | |
| 4 | Bulkhead valve (exhaust) | | | | | | | | |
| 5 | -Cartridge Valve Actuator 1- \\ | | | | | | | | |
| 6 | -Cylinder latch- \\ | | | | | | | | |
| 7 | A/M Valve 1 \\ | | | | | | | | |
| 8 | A/M Valve 2 \\ | | | | | | | | |
| 9 | A/M Valve 3 | | | | | | | | |
| 10 | A/M Valve 4 | | | | | | | | |
| 11 | A/M Clamp \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |
\\

Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# AccelBiotech Slides

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables]
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables]
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[Present: Cheri, Scott, Doug, Brent, Jim

Absent:&nbsp; Chris S.


h3. Machine Builds

* PCB's for a core build have been sent to McLane.&nbsp; Scott working on cost calculation to send them.
* Doug has first Ti HV puck tops.&nbsp; Will work with Roman on whether they are appropriate.
* Cheri tasked with assembling a 'spare' kit and we will get this&nbsp; x3

h3. MFB&nbsp;


h3. Drifter


h3. Software


h3. Deep ESP/DWSM

* Over weekend, water was inadvertently let into the sphere (~500ml) due to the wrong puck (LAF) being loaded.&nbsp; All things looked okay, until we tried the next SH1, and the puck heater started giving wild readings.&nbsp; It is probably fried.&nbsp; We will run some core negative PCRs, and recover next week (Tuesday) if weather permits.

h3. GUI


h3. Deployment Issues

* Brent working on networking the pier deployment.&nbsp; Will acquire larger antenna(s) and working on VPN issues.&nbsp; Possible trip down there Weds.&nbsp; Deployment looking to be during the week of the 19th.
* Doug will talk to science about designing the Pier-water Introduction System (PIS).

h3. &nbsp;Other Items

* Harbans Dhadwal (Stoney Brook, NY) will be&nbsp; visiting Friday, Oct 30.&nbsp; He'll be learning about basic MFB functions.&nbsp; Will need a 'cheat sheet' of commands, and maybe the 'training' can used colored water.&nbsp; Cheri on this.]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://predator.shore.mbari.org/esp_gui/launch.jnlp]

h3. Project Documentation:

h3. Other Documents
# [Documents|ProjectDocuments]
# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
## [ESP GUI Demo and Questions|2007_09_05]
## [Follow up meeting on Resources and Consumables|2008_01_08]
# [Presentations|ProjectPresentations]
# [Tasks]
# [Data Model]
# [Developer Documentation]

h3. Bug Tracking
# [JIRA Issue Tracker|http://oceana.shore.mbari.org:8082/browse/ESPAPP]

]]></property>
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<property name="body"><![CDATA[h4.


h4. {color:#ff00cc}SCRIPPS \-\- ESP-Waldo{color}

*&nbsp;April 27, 2015*

Roman delivers ESP Waldo to Andy Allen's lab at CVGI.&nbsp; Idea was to collect archived sample twice/week for \~6 months to test longevity issues with filters.

mid-June, instrument started losing comms to elevator dwarf.&nbsp; Roman sent down to replace dwarf on June 29-30. Re-canned and restarted mission

h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce. Divers: Kim R., Paul C.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

Divers: Paul C., Jeff Sevadjian

{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload. Divers: Eric R, Jeff Sevadjian
\\

h4. {color:#ff00cc}1st MAKAI flight w 5 cartridges{color}

*July 22, 2015*

Flew triangle pattern after launch.&nbsp; Makai found chlorophyll feature, and we fired two cartridges while flying through.&nbsp; First cartridge may have had sticky valve and stayed in by-pass (filtered 1L in \~20 minutes; too fast).&nbsp; Second cartridge seemed to have worked.

Some issues with ESP not communicating it was on, and then LRAUV not turning it on.&nbsp; Went to recover vehicle late July 23, but did not surface until mission timed-out, after we were already ashore.&nbsp; That was when we discovered the comms issues.&nbsp; Fixed one, tried to fire during a 'night operation' Thursday evening.&nbsp; Discovered Friday morning a second comms issues, which was fixed, and fired the 3 samples during day on Friday, July 24.&nbsp; Did keep-station all weekend, and recovered LRAUV early Monday morning (July 27).

Results:

1.&nbsp; Cartridge #1 bypassed 1L (toroid valve stuck; sea water ran through instrument in bypass mode; 7 minutes); flying through feature (chl=3.0 ug/l; 10.97m)

2. &nbsp; #2 filtered 815.8ml; flying through feature (11.03m; chl=3.3 ug/l; took 53 minutes)

3. &nbsp; #3 filtered 802.3ml;&nbsp; within feature (13.8m; chl=3.02 ug/l; took 51 minutes)

4. &nbsp; #4 filtered 759.6ml,&nbsp; above feature (7.1m; chl=1.11 ug/l; took 50 minutes)

5.&nbsp;&nbsp; #5 filtered 809.1ml,&nbsp; below feature (19.4m; chl=4.24 ug/l; took 51 minutes)

EXCELLENT summary paper by Yanwu Zhang about what the LRAUV did during this deployment-\-[here|^here|Yanwu's paper]. ]]></property>
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<property name="body"><![CDATA[h5. Questions

# How are volumes for duplicate phases handled?
# Script gets generated but not in sync with timing of simulator/instrument, how to best synch:
{noformat}
CH.stop
I2C::MsgErr in sampler -- I2C::Servo::OffCmd Not yet modeled
I2C::MsgErr in storage -- I2C::Servo::OffCmd Not yet modeled
I2C::MsgErr in sampler -- I2C::Servo::ConfigureCmd Not yet modeled
I2C::MsgErr in storage -- I2C::Servo::ConfigureCmd Not yet modeled
CH.configure CHconfig
PH.stop
PH.configure PHconfig
Posix::Error in quick -- /dev/ctd not a character device
Starting with tube #2
delayUntil "06:15:00.00 PDT 13-Mar-08"
@06:15:00.00PDT13-Mar-08 <poll> CTD.startLogging
@06:15:00.00 <quick> Initial Intake Purge
@06:16:30.00 ==> hab 1000ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@09:46:30.00 Disinfect Intake
@09:48:30.00 Shutdown
delayUntil "13:50:00.00"
@12:15:00.00 <poll> CTD.update
@13:50:00.00 <quick> ==> bac 900ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@17:20:00.00 Disinfect Intake
@17:22:00.00 Shutdown
delayUntil "01:25:00.00 PDT 14-Mar-08"
@18:15:00.00 <poll> CTD.update
@00:15:00.00PDT14-Mar-08 CTD.update
@01:25:00.00 <quick> Initial Intake Purge
@01:26:30.00 ==> larv 900ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@04:56:30.00 Disinfect Intake
@04:58:30.00 Shutdown
delayUntil "11:20:00.00"
@06:15:00.00 <poll> CTD.update
@11:20:00.00 <quick> Initial Intake Purge
@11:21:30.00 ==> da 1000ml, :image=>[:hires, 15, :default, 4, :midres, :auto]
@12:15:00.00 <poll> CTD.update
@14:21:30.00 <quick> Disinfect Intake
@14:23:30.00 Shutdown
delayUntil "20:30:00.00"
@18:15:00.00 <poll> CTD.update
@20:30:00.00 <quick> Initial Intake Purge
@20:31:30.00 ==> hab 1000ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@00:01:30.00PDT15-Mar-08 ==> da 1000ml, :image=>[:hires, 15, :default, 4, :midres, :auto]
@00:15:00.00 <poll> CTD.update
@02:01:30.00 <quick> Disinfect Intake
@02:03:30.00 Shutdown
gui_test.rb Assays Completed. CTD logging continues ... 
delayUntil "00:13:07.00"
Schedule::Error in quick -- Delay::RunEvent for @00:13:07.00 PDT 15-Mar-08 is in the past
Waiting to Resume from Checkpoint "gui_test.rb Assays Completed. CTD logging continues ... "
@06:15:00.00 <poll> CTD.update
@12:15:00.00 CTD.update
@18:15:00.00 CTD.update
@00:15:00.00PDT16-Mar-08 CTD.update
{noformat}]]></property>
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<id name="id">3179413</id>
<property name="body"><![CDATA[h5. Questions

# Script gets generated but not in sync with timing of simulator/instrument, how to best synch:
{noformat}
CH.stop
I2C::MsgErr in sampler -- I2C::Servo::OffCmd Not yet modeled
I2C::MsgErr in storage -- I2C::Servo::OffCmd Not yet modeled
I2C::MsgErr in sampler -- I2C::Servo::ConfigureCmd Not yet modeled
I2C::MsgErr in storage -- I2C::Servo::ConfigureCmd Not yet modeled
CH.configure CHconfig
PH.stop
PH.configure PHconfig
Posix::Error in quick -- /dev/ctd not a character device
Starting with tube #2
delayUntil "06:15:00.00 PDT 13-Mar-08"
@06:15:00.00PDT13-Mar-08 <poll> CTD.startLogging
@06:15:00.00 <quick> Initial Intake Purge
@06:16:30.00 ==> hab 1000ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@09:46:30.00 Disinfect Intake
@09:48:30.00 Shutdown
delayUntil "13:50:00.00"
@12:15:00.00 <poll> CTD.update
@13:50:00.00 <quick> ==> bac 900ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@17:20:00.00 Disinfect Intake
@17:22:00.00 Shutdown
delayUntil "01:25:00.00 PDT 14-Mar-08"
@18:15:00.00 <poll> CTD.update
@00:15:00.00PDT14-Mar-08 CTD.update
@01:25:00.00 <quick> Initial Intake Purge
@01:26:30.00 ==> larv 900ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@04:56:30.00 Disinfect Intake
@04:58:30.00 Shutdown
delayUntil "11:20:00.00"
@06:15:00.00 <poll> CTD.update
@11:20:00.00 <quick> Initial Intake Purge
@11:21:30.00 ==> da 1000ml, :image=>[:hires, 15, :default, 4, :midres, :auto]
@12:15:00.00 <poll> CTD.update
@14:21:30.00 <quick> Disinfect Intake
@14:23:30.00 Shutdown
delayUntil "20:30:00.00"
@18:15:00.00 <poll> CTD.update
@20:30:00.00 <quick> Initial Intake Purge
@20:31:30.00 ==> hab 1000ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@00:01:30.00PDT15-Mar-08 ==> da 1000ml, :image=>[:hires, 15, :default, 4, :midres, :auto]
@00:15:00.00 <poll> CTD.update
@02:01:30.00 <quick> Disinfect Intake
@02:03:30.00 Shutdown
gui_test.rb Assays Completed. CTD logging continues ... 
delayUntil "00:13:07.00"
Schedule::Error in quick -- Delay::RunEvent for @00:13:07.00 PDT 15-Mar-08 is in the past
Waiting to Resume from Checkpoint "gui_test.rb Assays Completed. CTD logging continues ... "
@06:15:00.00 <poll> CTD.update
@12:15:00.00 CTD.update
@18:15:00.00 CTD.update
@00:15:00.00PDT16-Mar-08 CTD.update
{noformat}]]></property>
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<property name="body"><![CDATA[h4.


h4. {color:#ff00cc}SCRIPPS \-\- ESP-Waldo{color}

*&nbsp;April 27, 2015*

Roman delivers ESP Waldo to Andy Allen's lab at CVGI.&nbsp; Idea was to collect archived sample twice/week for \~6 months to test longevity issues with filters.

mid-June, instrument started losing comms to elevator dwarf.&nbsp; Roman sent down to replace dwarf on June 29-30. Re-canned and restarted mission


h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce. Divers: Kim R., Paul C.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

Divers: Paul C., Jeff Sevadjian

{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload. Divers: Eric R, Jeff Sevadjian
\\

h4. {color:#ff00cc}1st MAKAI flight w 5 cartridges{color}

*July 22, 2015*

Flew triangle pattern after launch.&nbsp; Makai found chlorophyll feature, and we fired two cartridges while flying through.&nbsp; First cartridge may have had sticky valve and stayed in by-pass (filtered 1L in \~20 minutes; too fast).&nbsp; Second cartridge seemed to have worked.

Some issues with ESP not communicating it was on, and then LRAUV not turning it on.&nbsp; Went to recover vehicle late July 23, but did not surface until mission timed-out, after we were already ashore.&nbsp; That was when we discovered the comms issues.&nbsp; Fixed one, tried to fire during a 'night operation' Thursday evening.&nbsp; Discovered Friday morning a second comms issues, which was fixed, and fired the 3 samples during day on Friday, July 24.&nbsp; Did keep-station all weekend, and recovered LRAUV early Monday morning (July 27).

Results:

1.&nbsp; Cartridge #1 bypassed 1L (toroid valve stuck; sea water ran through instrument in bypass mode; 7 minutes); flying through feature (chl=3.0 ug/l; 10.97m)

2. &nbsp; #2 filtered 815.8ml; flying through feature (11.03m; chl=3.3 ug/l; took 53 minutes)

3. &nbsp; #3 filtered 802.3ml;&nbsp; within feature (13.8m; chl=3.02 ug/l; took 51 minutes)

4. &nbsp; #4 filtered 759.6ml,&nbsp; above feature (7.1m; chl=1.11 ug/l; took 50 minutes)

5.&nbsp;&nbsp; #5 filtered 809.1ml,&nbsp; below feature (19.4m; chl=4.24 ug/l; took 51 minutes)]]></property>
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<property name="body"><![CDATA[h5. Comments

# Have capability to add comments to phases that show up in script. Maybe go out in log too.
# Modify protocol so it doesn't kill between phases (want capability to call out alternate purge).
# Always odd things (give it ruby and time to run and it puts it in script).
# Phases should be different colors
# BUG: If delete last phase, can't add one at end.

h5. Questions

# How are volumes for duplicate phases handled?
{noformat}
# Sample Volumes for Assay Types
$habVol=1000
$larvVol=900
$larvVol=700
$daVol=30

startTube 2
# require '08feb'


startAt "14:44:34 03/12/2008"

initialPurge
hab
napUntil "10:05:13 03/13/2008"

larv
napUntil "05:50:00 03/14/2008"

initialPurge
larv
napUntil "17:45:00 03/14/2008"

da
shutdown
{noformat}
# Script gets generated but not in sync with timing of simulator/instrument, how to best synch:
{noformat}
CH.stop
I2C::MsgErr in sampler -- I2C::Servo::OffCmd Not yet modeled
I2C::MsgErr in storage -- I2C::Servo::OffCmd Not yet modeled
I2C::MsgErr in sampler -- I2C::Servo::ConfigureCmd Not yet modeled
I2C::MsgErr in storage -- I2C::Servo::ConfigureCmd Not yet modeled
CH.configure CHconfig
PH.stop
PH.configure PHconfig
Posix::Error in quick -- /dev/ctd not a character device
Starting with tube #2
delayUntil "06:15:00.00 PDT 13-Mar-08"
@06:15:00.00PDT13-Mar-08 <poll> CTD.startLogging
@06:15:00.00 <quick> Initial Intake Purge
@06:16:30.00 ==> hab 1000ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@09:46:30.00 Disinfect Intake
@09:48:30.00 Shutdown
delayUntil "13:50:00.00"
@12:15:00.00 <poll> CTD.update
@13:50:00.00 <quick> ==> bac 900ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@17:20:00.00 Disinfect Intake
@17:22:00.00 Shutdown
delayUntil "01:25:00.00 PDT 14-Mar-08"
@18:15:00.00 <poll> CTD.update
@00:15:00.00PDT14-Mar-08 CTD.update
@01:25:00.00 <quick> Initial Intake Purge
@01:26:30.00 ==> larv 900ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@04:56:30.00 Disinfect Intake
@04:58:30.00 Shutdown
delayUntil "11:20:00.00"
@06:15:00.00 <poll> CTD.update
@11:20:00.00 <quick> Initial Intake Purge
@11:21:30.00 ==> da 1000ml, :image=>[:hires, 15, :default, 4, :midres, :auto]
@12:15:00.00 <poll> CTD.update
@14:21:30.00 <quick> Disinfect Intake
@14:23:30.00 Shutdown
delayUntil "20:30:00.00"
@18:15:00.00 <poll> CTD.update
@20:30:00.00 <quick> Initial Intake Purge
@20:31:30.00 ==> hab 1000ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@00:01:30.00PDT15-Mar-08 ==> da 1000ml, :image=>[:hires, 15, :default, 4, :midres, :auto]
@00:15:00.00 <poll> CTD.update
@02:01:30.00 <quick> Disinfect Intake
@02:03:30.00 Shutdown
gui_test.rb Assays Completed. CTD logging continues ... 
delayUntil "00:13:07.00"
Schedule::Error in quick -- Delay::RunEvent for @00:13:07.00 PDT 15-Mar-08 is in the past
Waiting to Resume from Checkpoint "gui_test.rb Assays Completed. CTD logging continues ... "
@06:15:00.00 <poll> CTD.update
@12:15:00.00 CTD.update
@18:15:00.00 CTD.update
@00:15:00.00PDT16-Mar-08 CTD.update
{noformat}]]></property>
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<id name="id">3179416</id>
<property name="body"><![CDATA[h5. Questions

# How are volumes for duplicate phases handled?
{noformat}
# Sample Volumes for Assay Types
$habVol=1000
$larvVol=900
$larvVol=700
$daVol=30

startTube 2
# require '08feb'


startAt "14:44:34 03/12/2008"

initialPurge
hab
napUntil "10:05:13 03/13/2008"

larv
napUntil "05:50:00 03/14/2008"

initialPurge
larv
napUntil "17:45:00 03/14/2008"

da
shutdown
{noformat}
# Script gets generated but not in sync with timing of simulator/instrument, how to best synch:
{noformat}
CH.stop
I2C::MsgErr in sampler -- I2C::Servo::OffCmd Not yet modeled
I2C::MsgErr in storage -- I2C::Servo::OffCmd Not yet modeled
I2C::MsgErr in sampler -- I2C::Servo::ConfigureCmd Not yet modeled
I2C::MsgErr in storage -- I2C::Servo::ConfigureCmd Not yet modeled
CH.configure CHconfig
PH.stop
PH.configure PHconfig
Posix::Error in quick -- /dev/ctd not a character device
Starting with tube #2
delayUntil "06:15:00.00 PDT 13-Mar-08"
@06:15:00.00PDT13-Mar-08 <poll> CTD.startLogging
@06:15:00.00 <quick> Initial Intake Purge
@06:16:30.00 ==> hab 1000ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@09:46:30.00 Disinfect Intake
@09:48:30.00 Shutdown
delayUntil "13:50:00.00"
@12:15:00.00 <poll> CTD.update
@13:50:00.00 <quick> ==> bac 900ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@17:20:00.00 Disinfect Intake
@17:22:00.00 Shutdown
delayUntil "01:25:00.00 PDT 14-Mar-08"
@18:15:00.00 <poll> CTD.update
@00:15:00.00PDT14-Mar-08 CTD.update
@01:25:00.00 <quick> Initial Intake Purge
@01:26:30.00 ==> larv 900ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@04:56:30.00 Disinfect Intake
@04:58:30.00 Shutdown
delayUntil "11:20:00.00"
@06:15:00.00 <poll> CTD.update
@11:20:00.00 <quick> Initial Intake Purge
@11:21:30.00 ==> da 1000ml, :image=>[:hires, 15, :default, 4, :midres, :auto]
@12:15:00.00 <poll> CTD.update
@14:21:30.00 <quick> Disinfect Intake
@14:23:30.00 Shutdown
delayUntil "20:30:00.00"
@18:15:00.00 <poll> CTD.update
@20:30:00.00 <quick> Initial Intake Purge
@20:31:30.00 ==> hab 1000ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@00:01:30.00PDT15-Mar-08 ==> da 1000ml, :image=>[:hires, 15, :default, 4, :midres, :auto]
@00:15:00.00 <poll> CTD.update
@02:01:30.00 <quick> Disinfect Intake
@02:03:30.00 Shutdown
gui_test.rb Assays Completed. CTD logging continues ... 
delayUntil "00:13:07.00"
Schedule::Error in quick -- Delay::RunEvent for @00:13:07.00 PDT 15-Mar-08 is in the past
Waiting to Resume from Checkpoint "gui_test.rb Assays Completed. CTD logging continues ... "
@06:15:00.00 <poll> CTD.update
@12:15:00.00 CTD.update
@18:15:00.00 CTD.update
@00:15:00.00PDT16-Mar-08 CTD.update
{noformat}]]></property>
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<id name="id">28246080</id>
<property name="body"><![CDATA[h4.


h4. {color:#ff00cc}SCRIPPS \-\- ESP-Waldo{color}

*&nbsp;April 27, 2015*

Roman delivers ESP Waldo to Andy Allen's lab at CVGI.&nbsp; Idea was to collect archived sample twice/week for \~6 months to test longevity issues with filters.

mid-June, instrument started losing comms to elevator dwarf.&nbsp; Roman sent down to replace dwarf on June 29-30. Re-canned and restarted mission

h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce. Divers: Kim R., Paul C.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

Divers: Paul C., Jeff Sevadjian

{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload. Divers: Eric R, Jeff Sevadjian
\\

h4. {color:#ff00cc}1st MAKAI flight w 5 cartridges{color}

*July 22, 2015*

Flew triangle pattern after launch.&nbsp; Makai found chlorophyll feature, and we fired two cartridges while flying through.&nbsp; First cartridge may have had sticky valve and stayed in by-pass (filtered 1L in \~20 minutes; too fast).&nbsp; Second cartridge seemed to have worked.

Some issues with ESP not communicating it was on, and then LRAUV not turning it on.&nbsp; Went to recover vehicle late July 23, but did not surface until mission timed-out, after we were already ashore.&nbsp; That was when we discovered the comms issues.&nbsp; Fixed one, tried to fire during a 'night operation' Thursday evening.&nbsp; Discovered Friday morning a second comms issues, which was fixed, and fired the 3 samples during day on Friday, July 24.&nbsp; Did keep-station all weekend, and recovered LRAUV early Monday morning (July 27).

Results:

1.&nbsp; Cartridge #1 bypassed 1L (toroid valve stuck; sea water ran through instrument in bypass mode; 7 minutes); flying through feature (chl=3.0 ug/l; 10.97m)

2. &nbsp; #2 filtered 815.8ml; flying through feature (11.03m; chl=3.3 ug/l; took 53 minutes)

3. &nbsp; #3 filtered 802.3ml;&nbsp; within feature (13.8m; chl=3.02 ug/l; took 51 minutes)

4. &nbsp; #4 filtered 759.6ml,&nbsp; above feature (7.1m; chl=1.11 ug/l; took 50 minutes)

5.&nbsp;&nbsp; #5 filtered 809.1ml,&nbsp; below feature (19.4m; chl=4.24 ug/l; took 51 minutes)

EXCELLENT summary paper by Yanwu Zhang about what the LRAUV did during this deployment--[here|^Zhang_etal_chlpeak.pdf|Yanwu's paper]. ]]></property>
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<property name="body"><![CDATA[h5. Comments

# Have capability to add comments to phases that show up in script. Maybe go out in log too. Also add header comments. (global too).
# Modify protocol so it doesn't kill between phases (want capability to call out alternate purge).
# Always odd things (give it ruby and time to run and it puts it in script).
# Phases should be different colors
# BUG: If delete last phase, can't add one at end.
# Need to specify a way just to sequence things, not deterministic time.
# Have way to call out initial purge instead of upper/lowercase

h5. Questions

# How are volumes for duplicate phases handled?
{noformat}
# Sample Volumes for Assay Types
$habVol=1000
$larvVol=900
$larvVol=700
$daVol=30

startTube 2
# require '08feb'


startAt "14:44:34 03/12/2008"

initialPurge
hab
napUntil "10:05:13 03/13/2008"

larv
napUntil "05:50:00 03/14/2008"

initialPurge
larv
napUntil "17:45:00 03/14/2008"

da
shutdown
{noformat}
# Script gets generated but not in sync with timing of simulator/instrument, how to best synch:
{noformat}
CH.stop
I2C::MsgErr in sampler -- I2C::Servo::OffCmd Not yet modeled
I2C::MsgErr in storage -- I2C::Servo::OffCmd Not yet modeled
I2C::MsgErr in sampler -- I2C::Servo::ConfigureCmd Not yet modeled
I2C::MsgErr in storage -- I2C::Servo::ConfigureCmd Not yet modeled
CH.configure CHconfig
PH.stop
PH.configure PHconfig
Posix::Error in quick -- /dev/ctd not a character device
Starting with tube #2
delayUntil "06:15:00.00 PDT 13-Mar-08"
@06:15:00.00PDT13-Mar-08 <poll> CTD.startLogging
@06:15:00.00 <quick> Initial Intake Purge
@06:16:30.00 ==> hab 1000ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@09:46:30.00 Disinfect Intake
@09:48:30.00 Shutdown
delayUntil "13:50:00.00"
@12:15:00.00 <poll> CTD.update
@13:50:00.00 <quick> ==> bac 900ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@17:20:00.00 Disinfect Intake
@17:22:00.00 Shutdown
delayUntil "01:25:00.00 PDT 14-Mar-08"
@18:15:00.00 <poll> CTD.update
@00:15:00.00PDT14-Mar-08 CTD.update
@01:25:00.00 <quick> Initial Intake Purge
@01:26:30.00 ==> larv 900ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@04:56:30.00 Disinfect Intake
@04:58:30.00 Shutdown
delayUntil "11:20:00.00"
@06:15:00.00 <poll> CTD.update
@11:20:00.00 <quick> Initial Intake Purge
@11:21:30.00 ==> da 1000ml, :image=>[:hires, 15, :default, 4, :midres, :auto]
@12:15:00.00 <poll> CTD.update
@14:21:30.00 <quick> Disinfect Intake
@14:23:30.00 Shutdown
delayUntil "20:30:00.00"
@18:15:00.00 <poll> CTD.update
@20:30:00.00 <quick> Initial Intake Purge
@20:31:30.00 ==> hab 1000ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@00:01:30.00PDT15-Mar-08 ==> da 1000ml, :image=>[:hires, 15, :default, 4, :midres, :auto]
@00:15:00.00 <poll> CTD.update
@02:01:30.00 <quick> Disinfect Intake
@02:03:30.00 Shutdown
gui_test.rb Assays Completed. CTD logging continues ... 
delayUntil "00:13:07.00"
Schedule::Error in quick -- Delay::RunEvent for @00:13:07.00 PDT 15-Mar-08 is in the past
Waiting to Resume from Checkpoint "gui_test.rb Assays Completed. CTD logging continues ... "
@06:15:00.00 <poll> CTD.update
@12:15:00.00 CTD.update
@18:15:00.00 CTD.update
@00:15:00.00PDT16-Mar-08 CTD.update
{noformat}]]></property>
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<property name="body"><![CDATA[h4.


h4. {color:#ff00cc}SCRIPPS \-\- ESP-Waldo{color}

*&nbsp;April 27, 2015*

Roman delivers ESP Waldo to Andy Allen's lab at CVGI.&nbsp; Idea was to collect archived sample twice/week for \~6 months to test longevity issues with filters.

mid-June, instrument started losing comms to elevator dwarf.&nbsp; Roman sent down to replace dwarf on June 29-30. Re-canned and restarted mission

h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce. Divers: Kim R., Paul C.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

Divers: Paul C., Jeff Sevadjian

{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload. Divers: Eric R, Jeff Sevadjian
\\

h4. {color:#ff00cc}1st MAKAI flight w 5 cartridges{color}

*July 22, 2015*

Flew triangle pattern after launch.&nbsp; Makai found chlorophyll feature, and we fired two cartridges while flying through.&nbsp; First cartridge may have had sticky valve and stayed in by-pass (filtered 1L in \~20 minutes; too fast).&nbsp; Second cartridge seemed to have worked.

Some issues with ESP not communicating it was on, and then LRAUV not turning it on.&nbsp; Went to recover vehicle late July 23, but did not surface until mission timed-out, after we were already ashore.&nbsp; That was when we discovered the comms issues.&nbsp; Fixed one, tried to fire during a 'night operation' Thursday evening.&nbsp; Discovered Friday morning a second comms issues, which was fixed, and fired the 3 samples during day on Friday, July 24.&nbsp; Did keep-station all weekend, and recovered LRAUV early Monday morning (July 27).

Results:

1.&nbsp; Cartridge #1 bypassed 1L (toroid valve stuck; sea water ran through instrument in bypass mode; 7 minutes); flying through feature (chl=3.0 ug/l; 10.97m)

2. &nbsp; #2 filtered 815.8ml; flying through feature (11.03m; chl=3.3 ug/l; took 53 minutes)

3. &nbsp; #3 filtered 802.3ml;&nbsp; within feature (13.8m; chl=3.02 ug/l; took 51 minutes)

4. &nbsp; #4 filtered 759.6ml,&nbsp; above feature (7.1m; chl=1.11 ug/l; took 50 minutes)

5.&nbsp;&nbsp; #5 filtered 809.1ml,&nbsp; below feature (19.4m; chl=4.24 ug/l; took 51 minutes)

EXCELLENT summary paper by Yanwu Zhang about what the LRAUV did during this deployment-\-[here|^Zhang_etal_chlpeak.pdf\|Yanwu's paper\]. ]]></property>
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<property name="body"><![CDATA[h4.


h4. {color:#ff00cc}SCRIPPS \-\- ESP-Waldo{color}

*&nbsp;April 27, 2015*

Roman delivers ESP Waldo to Andy Allen's lab at CVGI.&nbsp; Idea was to collect archived sample twice/week for \~6 months to test longevity issues with filters.

mid-June, instrument started losing comms to elevator dwarf.&nbsp; Roman sent down to replace dwarf on June 29-30. Re-canned and restarted mission

h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce. Divers: Kim R., Paul C.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

Divers: Paul C., Jeff Sevadjian

{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload. Divers: Eric R, Jeff Sevadjian
\\

h4. {color:#ff00cc}1st MAKAI flight w 5 cartridges{color}

*July 22, 2015*

Flew triangle pattern after launch.&nbsp; Makai found chlorophyll feature, and we fired two cartridges while flying through.&nbsp; First cartridge may have had sticky valve and stayed in by-pass (filtered 1L in \~20 minutes; too fast).&nbsp; Second cartridge seemed to have worked.

Some issues with ESP not communicating it was on, and then LRAUV not turning it on.&nbsp; Went to recover vehicle late July 23, but did not surface until mission timed-out, after we were already ashore.&nbsp; That was when we discovered the comms issues.&nbsp; Fixed one, tried to fire during a 'night operation' Thursday evening.&nbsp; Discovered Friday morning a second comms issues, which was fixed, and fired the 3 samples during day on Friday, July 24.&nbsp; Did keep-station all weekend, and recovered LRAUV early Monday morning (July 27).

Results:

1.&nbsp; Cartridge #1 bypassed 1L (toroid valve stuck; sea water ran through instrument in bypass mode; 7 minutes); flying through feature (chl=3.0 ug/l; 10.97m)

2. &nbsp; #2 filtered 815.8ml; flying through feature (11.03m; chl=3.3 ug/l; took 53 minutes)

3. &nbsp; #3 filtered 802.3ml;&nbsp; within feature (13.8m; chl=3.02 ug/l; took 51 minutes)

4. &nbsp; #4 filtered 759.6ml,&nbsp; above feature (7.1m; chl=1.11 ug/l; took 50 minutes)

5.&nbsp;&nbsp; #5 filtered 809.1ml,&nbsp; below feature (19.4m; chl=4.24 ug/l; took 51 minutes)

EXCELLENT summary paper by Yanwu Zhang about what the LRAUV did during this deployment-\-[here|Yanwu's paper]. ]]></property>
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<property name="body"><![CDATA[h4.


h4. {color:#ff00cc}SCRIPPS \-\- ESP-Waldo{color}

*&nbsp;April 27, 2015*

Roman delivers ESP Waldo to Andy Allen's lab at CVGI.&nbsp; Idea was to collect archived sample twice/week for \~6 months to test longevity issues with filters.

mid-June, instrument started losing comms to elevator dwarf.&nbsp; Roman sent down to replace dwarf on June 29-30. Re-canned and restarted mission

h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce. Divers: Kim R., Paul C.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

Divers: Paul C., Jeff Sevadjian

{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload. Divers: Eric R, Jeff Sevadjian
\\

h4. {color:#ff00cc}1st MAKAI flight w 5 cartridges{color}

*July 22, 2015*

Flew triangle pattern after launch.&nbsp; Makai found chlorophyll feature, and we fired two cartridges while flying through.&nbsp; First cartridge may have had sticky valve and stayed in by-pass (filtered 1L in \~20 minutes; too fast).&nbsp; Second cartridge seemed to have worked.

Some issues with ESP not communicating it was on, and then LRAUV not turning it on.&nbsp; Went to recover vehicle late July 23, but did not surface until mission timed-out, after we were already ashore.&nbsp; That was when we discovered the comms issues.&nbsp; Fixed one, tried to fire during a 'night operation' Thursday evening.&nbsp; Discovered Friday morning a second comms issues, which was fixed, and fired the 3 samples during day on Friday, July 24.&nbsp; Did keep-station all weekend, and recovered LRAUV early Monday morning (July 27).

Results:

1.&nbsp; Cartridge #1 bypassed 1L (toroid valve stuck; sea water ran through instrument in bypass mode; 7 minutes); flying through feature (chl=3.0 ug/l; 10.97m)

2. &nbsp; #2 filtered 815.8ml; flying through feature (11.03m; chl=3.3 ug/l; took 53 minutes)

3. &nbsp; #3 filtered 802.3ml;&nbsp; within feature (13.8m; chl=3.02 ug/l; took 51 minutes)

4. &nbsp; #4 filtered 759.6ml,&nbsp; above feature (7.1m; chl=1.11 ug/l; took 50 minutes)

5.&nbsp;&nbsp; #5 filtered 809.1ml,&nbsp; below feature (19.4m; chl=4.24 ug/l; took 51 minutes)

EXCELLENT summary paper by Yanwu Zhang about what the LRAUV did during this deployment-\-[here|^Yanwu's paper]Zhang_etal_chlpeak.pdf\|Yanwu's paper\]. ]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Task Wish List b/w D-ESP deployments 27OCT--25NOV, 2009] <--\-{color:#ff0000}{*}NEW (Oct 7, 2009{*}{color})
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [Functional Requirements for Gen 3 ESP] <--\-{color:#ff0000}{*}NEW (July 15, 2009{*}{color})

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# 13Mar2008 (Teleconference with LLNL)
# 20Mar2008]]></property>
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</property>
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<property name="body"><![CDATA[D-ESP get retrieved October 26, 2009 and re-deployed November 26, 2009.

&nbsp;Below, add to the list of 'to-dos' before the November deployment back on MARS:
# &nbsp;]]></property>
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<property name="body"><![CDATA[D-ESP get retrieved October 26, 2009 and re-deployed November 26, 2009.

&nbsp;Below, add to the list of 'to-dos' before the November deployment back on MARS:
# Complete integration of Data Aqcuisition subsystem
# Ground Fault subsystem
# &nbsp;]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]]]></property>
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<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically+

April 6--Bruce at M0 for surface deployment (Zephyr)

April 15--Mack in Sphere for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

April 29--Recover Bruce at M0 (Zephyr)

May 1--Mack in sphere connected to DWSM(dive #3); incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

May 14--Deploy NEO w/PCR, surface deployment (Zephyr)

May 27--First Drifter dive (Zephyr)

June 5-9 \-\- Western Flyer.&nbsp; D-ESP, Drifter, and CTD casts. {color:#cc0000}{*}MOVIES{*}{color}:  D-ESP launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/DESP%20deployment%20(full%20quality).dv].  Drifter launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/Drifter.dv].

June 11 \-\- Recover NEO.&nbsp; (Zephyr)
\\

FALL Network Deployment

Proposed locations are here: [http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&msid=113879459163411006053.000471828af997bd7d89c&t=h&z=12]

September 24 \-\- Deploy Moe w/PCR at M0.&nbsp; Deployed Mack at Santa Cruz.&nbsp; Deployed Bruce in the bight.&nbsp; (Zephyr)&nbsp; Lost communications with Bruce that day.

September 28 \-\- Recover (dead) Bruce.&nbsp; Comms box had water in it, but radio worked.&nbsp; EM cable had 2 broken wires. (Zephyr)

September 30 \-\- Deploy D-ESP on MARS (Lobos).&nbsp; Hand issue at first, but 'fixed' itself.]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# 13Mar2008
# 20Mar2008]]></property>
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</property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [Functional Requirements for Gen 3 ESP] <--\-{color:#ff0000}{*}NEW (July 15, 2009{*}{color})

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10389137</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Task Wish List b/w D-ESP deployments 27OCT--25NOV, 2009]<--\-{color:#ff0000}{*}NEW (Oct 7, 2009{*}{color})
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [Functional Requirements for Gen 3 ESP] <--\-{color:#ff0000}{*}NEW (July 15, 2009{*}{color})

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the G3 ESP and LRAUV Integration Page

\\

h3. Interface Control Documents

[3G-LRAUV ICD ver1-0.doc]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the G3 ESP and LRAUV Integration Page

\\

h3. Interface Control Documents
3G-LRAUV ICD ver1-0.doc]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3-LRAUV ICD ver 1.0|https://oceana.mbari.org/confluence/download/attachments/2162822/3G-LRAUV+ICD+ver1-0.doc]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration|https://oceana.mbari.org/confluence/download/attachments/2162822/3G-LRAUV+ICD+ver1-0.doc]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [|https://oceana.mbari.org/confluence/download/attachments/2162822/3G-LRAUV+ICD+ver1-0.doc][G3 - LRAUV Integration]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[4.  Investigate remaining puck handling problems warm and cold

\-\- still seeing Elbow errors even when Forearm not pressing puck against backstop

5.  Add software check to ensure mission continuation's startTube matches last used

6.    Consider adding a thin o-ring to seal LAF pucks in clamps

7.  Cool oil down to 3C and check its viscosity

8.  Determine why sphere appears to be electrically connected to frame

9.  Try to determine how much gas is dissolved in our silicon oil

\-\-  does this explain pressure increasing slowly during sampling?]]></property>
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<property name="body"><![CDATA[h1. Welcome to the G3 ESP and LRAUV Integration Page]]></property>
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<property name="body"><![CDATA[h1. Welcome to the G3 ESP and LRAUV Integration Page
\\

h3. Interface Control Documents
\\]]></property>
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<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically+

April 6--Bruce at M0 for surface deployment (Zephyr)

April 15--Mack in Sphere for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

April 29--Recover Bruce at M0 (Zephyr)

May 1--Mack in sphere connected to DWSM(dive #3); incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

May 14--Deploy NEO w/PCR, surface deployment (Zephyr)

May 27--First Drifter dive (Zephyr)

June 5-9 \-\- Western Flyer.&nbsp; D-ESP, Drifter, and CTD casts. {color:#cc0000}{*}MOVIES{*}{color}:  D-ESP launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/DESP%20deployment%20(full%20quality).dv].  Drifter launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/Drifter.dv].

June 11 \-\- Recover NEO.&nbsp; (Zephyr)\\

FALL Network Deployment

Proposed locations are here: http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&msid=113879459163411006053.000471828af997bd7d89c&t=h&z=12 ]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began

*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).
Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays
Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

MELO used was #300034012090780

location reported by MELO was-\- &nbsp; 33.4865 \-118.51285

*March 20*\--lost comms

*March 21*\--re-established comms and think problem in E/M cable.

*March 22*\--lost comms

*April 3*\--small boat to buoy to test E/M cable

*April 8*\--'rescue' mission. Swapped E/M cables and repositioned in slightly deeper water, at 33.48504 \-118.50988


h4. {color:#ff00cc}ECOHAB--S. California{color}

April 1--Instruments deployed

&nbsp;MOE--inshore at 33.60779 \-118.01877 with ISUS


Melo was 300234060014550

avg can depth \~9m\\

&nbsp;Bruce--offshore at 33.58609 \-118.03686


Melo was 300234060016190

avg can depth \~19.5m ]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2019Feb08.pdf]
# [Engineering Timeline]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science]]></property>
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<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically+

April 6--Bruce at M0 for surface deployment (Zephyr)

April 15--Mack in Sphere for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

April 29--Recover Bruce at M0 (Zephyr)

May 1--Mack in sphere connected to DWSM(dive #3); incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

May 14--Deploy NEO w/PCR, surface deployment (Zephyr)

May 27--First Drifter dive (Zephyr)

June 5-9 \-\- Western Flyer.&nbsp; D-ESP, Drifter, and CTD casts. {color:#cc0000}{*}MOVIES{*}{color}:  D-ESP launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/DESP%20deployment%20(full%20quality).dv].  Drifter launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/Drifter.dv].

June 11 \-\- Recover NEO.&nbsp; (Zephyr)
\\

FALL Network Deployment

Proposed locations are here: [http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&msid=113879459163411006053.000471828af997bd7d89c&t=h&z=12]

September 22 \-\- Deploy Moe w/PCR at M0.&nbsp; Deployed Mack at Santa Cruz.&nbsp; Deployed Bruce in the bight.&nbsp; (Zephyr)&nbsp; Lost communications with Bruce that day.

September 28 \-\- Recover (dead) Bruce.&nbsp; Comms box had water in it, but radio worked.&nbsp; EM cable had 2 broken wires. (Zephyr)


September 30 \-\- Deploy D-ESP on MARS (Lobos).&nbsp; Hand issue at first, but 'fixed' itself.]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2019Feb08.pdf]
# [Engineering Timeline]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [Some new page]

h2. Science]]></property>
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<property name="body"><![CDATA[These are some notes about the servo model design and implementation.

Here are some of the plots generated from the unit tests:

!test_similar_to_servoTest.png!  
                    
!test_absMoves_with_direction_change_before_stop.png!

!test_setRawLimits_and_abrupt_stop_overCurrent.png!  

!test_getTimesForLimits.png!    
                     
!test_CompositeFunction_simple.png!                       

h1. Design in a nutshell

At time of writing the code resides in the 'servomodel' branch:
   https://github.com/MBARI-ESP/ESP2Gscript/tree/servomodel

The main source file, where the {{I2C::Servo::Model}} class is defined is: [servomodel.rb|https://github.com/MBARI-ESP/ESP2Gscript/blob/b63f5de300c96e1d2e1f68f7ac13eab01fa3e7f5/lib/i2c/model/servomodel.rb].

The servo simulation is modularized in a layered way. Elements of the modeling itself are under the {{ServoModeling}} module:

- {{Servo::Model}} and related elements are only concerned, in terms of the characterization of the velocity-position function, with {{ServoChannelSimulator}}.

- {{ServoChannelSimulator}} makes use of a {{FunctionFactory}} to keep and adjust the overall velocity-position function according to move commands.

- {{FunctionFactory}} facilitates the construction of {{Function}}'s.

- Possible {{Function}}'s are:
-- {{ConstantFunction}}: function always evaluating to {{\[0, pos\]}} for a given position
-- {{MonotoneFunction}}: captures the basic velocity profile of starting at a given velocity, and then going through acceleration, plateau (each of which can be of zero duration), and deceleration zones. Starting at a given initial position, this function changes the position monotonically in a given direction.
-- {{CompositeFunction}}: function composed of the concatenation of multiple functions, each applied from a specific time wrt the previous one.


h1. Testing

All unit tests can be run at the command line as follows:

{code}
$ find test/lib/i2c/model -name \*_test.rb -exec ruby -I. -Ilib -Iutils -Itest/lib {} \;
Loaded suite test/lib/i2c/model/servo/function_test
Started
..........
Finished in 0.013645 seconds.

10 tests, 607 assertions, 0 failures, 0 errors
Loaded suite test/lib/i2c/model/servo/functionfact_test
Started
..........
Finished in 0.029115 seconds.

10 tests, 1068 assertions, 0 failures, 0 errors
Loaded suite test/lib/i2c/model/servo/servochannelsim_test
Started
.......
Finished in 0.08877 seconds.

7 tests, 2531 assertions, 0 failures, 0 errors
Loaded suite test/lib/i2c/model/servomodel_test
Started
.......
Finished in 0.188708 seconds.

7 tests, 184 assertions, 0 failures, 0 errors
{code}
]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2019Feb08.pdf]
# [Engineering Timeline]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science]]></property>
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<property name="body"><![CDATA[What]]></property>
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<id name="id">25428526</id>
<property name="body"><![CDATA[These are some notes about the servo model design and implementation.

Here are some of the plots generated from the unit tests:

!test_similar_to_servoTest.png!  
                    
!test_absMoves_with_direction_change_before_stop.png!

!test_setRawLimits_and_abrupt_stop_overCurrent.png!  

!test_getTimesForLimits.png!    
                     
!test_CompositeFunction_simple.png!                       

h1. Design in a nutshell

At time of writing the code resides in the 'servomodel' branch:
   https://github.com/MBARI-ESP/ESP2Gscript/tree/servomodel

The main source file, where the {{I2C::Servo::Model}} class is defined is: [servomodel.rb|https://github.com/MBARI-ESP/ESP2Gscript/blob/b63f5de300c96e1d2e1f68f7ac13eab01fa3e7f5/lib/i2c/model/servomodel.rb].

The servo simulation is modularized in a layered way. Elements of the modeling itself are under the {{ServoModeling}} module:

- {{Servo::Model}} and related elements are only concerned, in terms of the characterization of the velocity-position function, with {{ServoChannelSimulator}}.

- {{ServoChannelSimulator}} makes use of a {{FunctionFactory}} to keep and adjust the overall velocity-position function according to move commands.

- {{FunctionFactory}} facilitates the construction of {{Function}}'s.

- Possible {{Function}}'s are:
-- {{ConstantFunction}}: function always evaluating to {{\[0, pos\]}} for a given position
-- {{MonotoneFunction}}: captures the basic velocity profile of starting at a given velocity, and then going through acceleration, plateau (each of which can be of zero duration), and deceleration zones. Starting at a given initial position, this function changes the position monotonically in a given direction.
-- {{CompositeFunction}}: function composed of the concatenation of multiple functions, each applied from a specific time wrt the previous one.


h1. Testing

All unit tests can be run at the command line as follows:

{code}
$ find lib/i2c/model -name \*_test.rb -exec ruby -I. -Ilib -Iutils {} \;
Loaded suite lib/i2c/model/servo/function_test
Started
..........
Finished in 0.015772 seconds.

10 tests, 607 assertions, 0 failures, 0 errors
Loaded suite lib/i2c/model/servo/functionfact_test
Started
..........
Finished in 0.030916 seconds.

10 tests, 1068 assertions, 0 failures, 0 errors
Loaded suite lib/i2c/model/servo/servochannelsim_test
Started
.......
Finished in 0.087462 seconds.

7 tests, 2531 assertions, 0 failures, 0 errors
Loaded suite lib/i2c/model/servomodel_test
Started
.......
Finished in 0.199393 seconds.

7 tests, 184 assertions, 0 failures, 0 errors
{code}
]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2019Feb08.pdf]
# [Engineering Timeline]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [Some new page|NewPage]

h2. Science]]></property>
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h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2019Feb08.pdf]
# [Engineering Timeline]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# {color:#3300ff}+[{color:#3300ff}{+}Software cheat sheet{+}{color}|ESPAPP:Cheat Sheet]+{color}

h2. Science]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2019Feb08.pdf]
# [Engineering Timeline]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# {color:#3300ff}{+}Software cheat sheet{+}{color}

h2. Science]]></property>
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<property name="body"><![CDATA[Present: Chris S., Wayne, Chris P., Roman, Doug, Jim, Brent

Absent: Cheri, Scott

h3. Machine Builds

* NEO is ready for new lid.&nbsp; Needs bulkhead valves, brackets, and top of can fittings.&nbsp; Getting ready for pier deployment.&nbsp;
* Two of our radios need repair.&nbsp; Brent has RMO #s and will task Cheri with their return.

h3. MFB&nbsp;


h3. Drifter

* Jon Erickson's 2009 time on CMORE to design a 200m can is on-hold pending Gene's end-of-year review on drifter feasibility.

h3. Software


h3. Deep ESP/DWSM

* Doug's detective work found that the SS parts sitting in 2% bleach was causing rust, specifically crevice corrosion.&nbsp; Using more dilute bleach (0.2%) followed by water wash should be okay to the metal.

* We have a quote from FloTech for the Benthos ducer baffle.&nbsp; Will tell Hans told to order; charge $3600 to ASTEP II.

h3. GUI


h3. Deployment Issues

* &nbsp;Brent noticing hand jitter on both Moe (at M0) and Mack (at SC).&nbsp; Thinks its from belt tensioning changing and slower sampling rate of the firmware.&nbsp; These have slower 32hz sampling protocol in the firmware.&nbsp; Gordon has newer 64Hz, and tuning doesn't need to be so precise.
* Bruce's cable has been dissected, and it is thought the break in leads #1 and #2 occurred \~2 inches from the start of the bell termination housing on the bailer end of the EM cable.&nbsp; Jim Scholfield thinks he can get it re-terminated with the remaining EM cable to be ready next Thursday.&nbsp; This changes our plans for Bruce, which we will now try and 're'-deploy on Monday or Tuesday (Oct 12/13).&nbsp; Will check with Grech about which will work for DMO; maybe go with Shana Rae if needed.&nbsp; Roman will dunk radio-box looking for leak.
* D-ESP.&nbsp; After plugging in, hand seemed to jam a puck at top of stack #2.&nbsp; Brent and Scott seemed to fix it--it's now run 3 shuffle puck routines, and Brent has pumped water through the core.&nbsp; Mission will begin tonight.&nbsp; Ideas for figuring out why it did this was to cold-shock it in the van, and use dial indicators to see how much physical change cold actually induces.
* Brent noticed that when turning off power to DWSM, the compensating temp gauges in the new pressure sensors cool down, so when powered again, there is all sorts of funkiness while they re-warm.&nbsp; Decision is to leave Gordon on all the time.
* Chris P. published Gordon's mission [here(v4)|^GordonVer4ScheduleOct09.pdf].

* SC pier deployment.&nbsp; Pumps are both in Bldg B lab near the eyewash.&nbsp; Brent and Jim will go to Pier Weds to work on setting up communications.&nbsp; Meet with city officials next Weds about using their network to communicate with our system.
\\

h3. &nbsp;Other Items

* For those listed on the R&D 100 award, there will be a ESP TEAM PHOTO on Monday.&nbsp; Time still to be set-up with Todd.&nbsp; Stay tuned.&nbsp; ]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# G3-LRAUV ICD ver 1.0

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2019Feb08.pdf]
# [Engineering Timeline]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]

h2. Science]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp; ]]></property>
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<property name="body"><![CDATA[Present: Chris S., Wayne, Chris P., Roman, Doug, Jim, Brent

Absent: Cheri, Scott

h3. Machine Builds

* NEO is ready for new lid.&nbsp; Needs bulkhead valves, brackets, and top of can fittings.&nbsp; Getting ready for pier deployment.&nbsp;
* Two of our radios need repair.&nbsp; Brent has RMO #s and will task Cheri with their return.

h3. MFB&nbsp;




h3. Drifter

* Jon Erickson's 2009 time on CMORE to design a 200m can is on-hold pending Gene's end-of-year review on drifter feasibility.

h3. Software


h3. Deep ESP/DWSM

* Doug's detective work found that the SS parts sitting in 2% bleach was causing rust, specifically crevice corrosion.&nbsp; Using more dilute bleach (0.2%) followed by water wash should be okay to the metal.

* We have a quote from FloTech for the Benthos ducer baffle.&nbsp; Will tell Hans told to order; charge $3600 to ASTEP II.

h3. GUI




h3. Deployment Issues

* &nbsp;Brent noticing hand jitter on both Moe (at M0) and Mack (at SC).&nbsp; Thinks its from belt tensioning changing and slower sampling rate of the firmware.&nbsp; These have slower 32hz sampling protocol in the firmware.&nbsp; Gordon has newer 64Hz, and tuning doesn't need to be so precise.
* Bruce's cable has been dissected, and it is thought the break in leads #1 and #2 occurred \~2 inches from the start of the bell termination housing on the bailer end of the EM cable.&nbsp; Jim Scholfield thinks he can get it re-terminated with the remaining EM cable to be ready next Thursday.&nbsp; This changes our plans for Bruce, which we will now try and 're'-deploy on Monday or Tuesday (Oct 12/13).&nbsp; Will check with Grech about which will work for DMO; maybe go with Shana Rae if needed.&nbsp; Roman will dunk radio-box looking for leak.
* D-ESP.&nbsp; After plugging in, hand seemed to jam a puck at top of stack #2.&nbsp; Brent and Scott seemed to fix it--it's now run 3 shuffle puck routines, and Brent has pumped water through the core.&nbsp; Mission will begin tonight.&nbsp; Ideas for figuring out why it did this was to cold-shock it in the van, and use dial indicators to see how much physical change cold actually induces.
* Brent noticed that when turning off power to DWSM, the compensating temp gauges in the new pressure sensors cool down, so when powered again, there is all sorts of funkiness while they re-warm.&nbsp; Decision is to leave Gordon on all the time.
* Chris P. published Gordon's mission [here(v4)|^GordonVer4ScheduleOct09.pdf].

* SC pier deployment.&nbsp; Pumps are both in Bldg B lab near the eyewash.&nbsp; Brent and Jim will go to Pier Weds to work on setting up communications.&nbsp; Meet with city officials next Weds about using their network to communicate with our system.
\\

h3. &nbsp;Other Items]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2019Feb08.pdf]
# [Engineering Timeline]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheet Sheet|Cheat Sheet]

h2. Science]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp; 


h4. {color:#ff00cc}Puget Sound{color}
*June 20, 2013*\--Deployed Univ. British Columbia ESP and the Lummi Bay aquaculture site.]]></property>
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<property name="body"><![CDATA[Present: Chris S., Wayne, Chris P., Roman, Doug, Jim, Brent

Absent: Cheri, Scott


h3. Machine Builds


h3. MFB

* &nbsp;

h3. Drifter&nbsp;


h3. Software



h3. Deep ESP/DWSM

Rust issue

Hans told to order modem baffle



h3. GUI

* &nbsp;

h3. Deployment Issues

* &nbsp;Brent noticing hand jitter on both Moe (at M0) and Mack (at SC).&nbsp; Thinks its from belt tensioning changing and slower sampling rate of the firmware.&nbsp; These have slower 32hz sampling protocol in the firmware.&nbsp; Gordon has newer 64Hz, and tuning doesn't need to be so precise.
* Bruce's cable has been dissected, and it is thought the break in leads #1 and #2 occurred \~2 inches from the start of the bell housing on the bailer end of the EM cable.&nbsp; Jim Scholfield thinks he can get it re-terminated in the remaining EM cable in 3 days; ready next Thursday.&nbsp; This changes our plans for Bruce, which we will now try and 're'-deploy on Monday or Tuesday (Oct 12/13).&nbsp; Will check with Grech about which will work for DMO; maybe go with Shana Rae if needed.
* D-ESP.&nbsp; After plugging in, hand seemed to jam a puck at top of stack #2.&nbsp; Brent and Scott seemed to fix it--it's now run 3 shuffle puck routines, and Brent has pumped water through the core.&nbsp; Mission will begin tonight.&nbsp; Ideas for figuring out why it did this was to cold-shock it in the van, and use dial indicators to see how much physical change cold actually induces.
* Brent noticed that when turning off power to DWSM, the compensating temp gauges in the new pressure sensors cool down, so when powered again, there is all sorts of funkiness while they re-warm.&nbsp; Decision is to leave Gordon on all the time.
* Chris P. published Gordon's mission [here(v4)|^GordonVer4ScheduleOct09.pdf].

* Word given to Hans to order the baffle.\\

h3. &nbsp;Other Items

* &nbsp;]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2019Feb08.pdf]
# [Engineering Timeline]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# Software Cheet Sheet

h2. Science]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 28, 2008*

*11am-12*
Present: Doug, Chris S, Scott, Addie, Brian, Cheri

h3. Tech Transfer


h6. Discussion Items:

* Update on Mack: Mack is beautiful. Doing it's first full phase, right now.
* Mike Parker contacted about piezoprinter problems (holding down membrane, cutting out disks) and is designing solutions.&nbsp; Also will be approached about a puck holder.
* Puck Etching: Next batch to go out... 701312.06 Pucks
* New syringes:
* Screens and scintered frits: Leter coded frits were ordered ny Jim.

h3. MFB

Discussion Items:
* Weak pos on Mon, but nothing since. Found that reagents were dead. New reagents on the block now.
* LLNL replacing components on the new boards.
* April fecal water sample purification test.

h3. Software

Not discussed, Brent on vacation.

h3. Sphere and 4K DWSMS

* Sphere update
** {color:#000000}No word or update from Wah Chang.{color}

* {color:#000000}DWSM progress?{color}
** {color:#000000}Revisiting motor for pumps. Sampling condition would be very power inefficient. Should have a power budget and motor/pump nailed down in a week.{color}
** Doing torque testing of pump since most of power is lost in running friction for the LP pumps.
* {color:#000000}Battery boxes?&nbsp; IN{color}
* {color:#000000}Batteries oredered? Yes{color}

ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)
ACTION:&nbsp; New surface can lid discrepency, Jim was going to meet with Gene about it. (Jim)

h3. GUI Development

Brian had image handling questions...]]></property>
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<property name="body"><![CDATA[These are some notes about the servo model design and implementation.

Here are some of the plots generated from the unit tests:

| !test_similar_to_servoTest.png!  |  !test_absMoves_with_direction_change_before_stop.png! | 
| !test_setRawLimits_and_abrupt_stop_overCurrent.png!  | !test_getTimesForLimits.png!    | 
| !test_CompositeFunction_simple.png!                       | 

h1. Design in a nutshell

At time of writing the code resides in the 'servomodel' branch:
   https://github.com/MBARI-ESP/ESP2Gscript/tree/servomodel

The main source file, where the {{I2C::Servo::Model}} class is defined is: [servomodel.rb|https://github.com/MBARI-ESP/ESP2Gscript/blob/b63f5de300c96e1d2e1f68f7ac13eab01fa3e7f5/lib/i2c/model/servomodel.rb].

The servo simulation is modularized in a layered way. Elements of the modeling itself are under the {{ServoModeling}} module:

- {{Servo::Model}} and related elements are only concerned, in terms of the characterization of the velocity-position function, with {{ServoChannelSimulator}}.

- {{ServoChannelSimulator}} makes use of a {{FunctionFactory}} to keep and adjust the overall velocity-position function according to move commands.

- {{FunctionFactory}} facilitates the construction of {{Function}}'s.

- Possible {{Function}}'s are:
-- {{ConstantFunction}}: function always evaluating to {{\[0, pos\]}} for a given position
-- {{MonotoneFunction}}: captures the basic velocity profile of starting at a given velocity, and then going through acceleration, plateau (each of which can be of zero duration), and deceleration zones. Starting at a given initial position, this function changes the position monotonically in a given direction.
-- {{CompositeFunction}}: function composed of the concatenation of multiple functions, each applied from a specific time wrt the previous one.


h1. Testing

h2. Unit tests

All unit tests can be run at the command line as follows:

{code}
$ find test/lib/i2c/model -name \*_test.rb -exec ruby -I. -Ilib -Iutils -Itest/lib {} \;
Loaded suite test/lib/i2c/model/servo/function_test
Started
..........
Finished in 0.013645 seconds.

10 tests, 607 assertions, 0 failures, 0 errors
Loaded suite test/lib/i2c/model/servo/functionfact_test
Started
..........
Finished in 0.029115 seconds.

10 tests, 1068 assertions, 0 failures, 0 errors
Loaded suite test/lib/i2c/model/servo/servochannelsim_test
Started
.......
Finished in 0.08877 seconds.

7 tests, 2531 assertions, 0 failures, 0 errors
Loaded suite test/lib/i2c/model/servomodel_test
Started
.......
Finished in 0.188708 seconds.

7 tests, 184 assertions, 0 failures, 0 errors
{code}

h2. Test with actual integration in the framework

The following tested in both {{simfast}} and {{simreal}} modes:

{code}
carueda@bufflehead:~/esp2$ . bin/ESPenv shallow moe
carueda@bufflehead:~/esp2$ ESPmode=simfast
carueda@bufflehead:~/esp2$ esp
ESPmoe:001:0-> require 'plot'
true
ESPmoe:002:0-> ssLog = SS.log {SS.home.empty; SS.fill}
SS.reconfigure SSconfig
SS.home.seek empty
@16:00:00.82 SS.seek 25.00ml
[<I2C::Servo::Status enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=-12, velocity=-12, current=0, pwm=0, err=0, inPress=0, outPress=0, deltaPress=0, voltage=12.1620363279332>,
...
 <I2C::Servo::Status enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=108084, velocity=12, current=0, pwm=0, err=0, inPress=0, outPress=0, deltaPress=0, voltage=12.1620363279332>,
 <I2C::Servo::Status enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=108096, velocity=0, current=0, pwm=0, err=0, inPress=0, outPress=0, deltaPress=0, voltage=12.1620363279332>]
ESPmoe:003:0-> plot ssLog
#<Thread::PLOT_1 priority=1 sleep>
ESPmoe:004:0->
{code}

The generated plot:
!servosim-quickplot-1.png!
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<property name="body"><![CDATA[Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note that we have yet to make a full batch of high-volume snap pucks, but when we do, those will be labeled 1HV (top and bottom).

Here is who is doing our etching:

LaserMark
2109 O'Toole Ave. Ste S
San Jose, CA 95131
Phone 408 433-9333
Fax 408 433-9343 ]]></property>
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<property name="body"><![CDATA[These are some notes about the servo model design and implementation.

Here are some of the plots generated from the unit tests:

!test_similar_to_servoTest.png!  
                    
!test_absMoves_with_direction_change_before_stop.png!

!test_setRawLimits_and_abrupt_stop_overCurrent.png!  

!test_getTimesForLimits.png!    
                     
!test_CompositeFunction_simple.png!                       

h1. Design in a nutshell

At time of writing the code resides in the 'servomodel' branch:
   https://github.com/MBARI-ESP/ESP2Gscript/tree/servomodel

The main source file, where the {{I2C::Servo::Model}} class is defined is: [servomodel.rb|https://github.com/MBARI-ESP/ESP2Gscript/blob/b63f5de300c96e1d2e1f68f7ac13eab01fa3e7f5/lib/i2c/model/servomodel.rb].

The servo simulation is modularized in a layered way. Elements of the modeling itself are under the {{ServoModeling}} module:

- {{Servo::Model}} and related elements are only concerned, in terms of the characterization of the velocity-position function, with {{ServoChannelSimulator}}.

- {{ServoChannelSimulator}} makes use of a {{FunctionFactory}} to keep and adjust the overall velocity-position function according to move commands.

- {{FunctionFactory}} facilitates the construction of {{Function}}'s.

- Possible {{Function}}'s are:
-- {{ConstantFunction}}: function always evaluating to {{\[0, pos\]}} for a given position
-- {{MonotoneFunction}}: captures the basic velocity profile of starting at a given velocity, and then going through acceleration, plateau (each of which can be of zero duration), and deceleration zones. Starting at a given initial position, this function changes the position monotonically in a given direction.
-- {{CompositeFunction}}: function composed of the concatenation of multiple functions, each applied from a specific time wrt the previous one.


h1. Testing

h2. Unit tests

All unit tests can be run at the command line as follows:

{code}
$ find test/lib/i2c/model -name \*_test.rb -exec ruby -I. -Ilib -Iutils -Itest/lib {} \;
Loaded suite test/lib/i2c/model/servo/function_test
Started
..........
Finished in 0.013645 seconds.

10 tests, 607 assertions, 0 failures, 0 errors
Loaded suite test/lib/i2c/model/servo/functionfact_test
Started
..........
Finished in 0.029115 seconds.

10 tests, 1068 assertions, 0 failures, 0 errors
Loaded suite test/lib/i2c/model/servo/servochannelsim_test
Started
.......
Finished in 0.08877 seconds.

7 tests, 2531 assertions, 0 failures, 0 errors
Loaded suite test/lib/i2c/model/servomodel_test
Started
.......
Finished in 0.188708 seconds.

7 tests, 184 assertions, 0 failures, 0 errors
{code}

h2. Integration tests

{code}
carueda@bufflehead:~/esp2$ . bin/ESPenv shallow moe
carueda@bufflehead:~/esp2$ ESPmode=simfast
carueda@bufflehead:~/esp2$ esp
ESPmoe:001:0-> require 'plot'
true
ESPmoe:002:0-> ssLog = SS.log {SS.home.empty; SS.fill}
SS.reconfigure SSconfig
SS.home.seek empty
@16:00:00.82 SS.seek 25.00ml
[<I2C::Servo::Status enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=-12, velocity=-12, current=0, pwm=0, err=0, inPress=0, outPress=0, deltaPress=0, voltage=12.1620363279332>,
...
 <I2C::Servo::Status enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=108084, velocity=12, current=0, pwm=0, err=0, inPress=0, outPress=0, deltaPress=0, voltage=12.1620363279332>,
 <I2C::Servo::Status enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=108096, velocity=0, current=0, pwm=0, err=0, inPress=0, outPress=0, deltaPress=0, voltage=12.1620363279332>]
ESPmoe:003:0-> plot ssLog
#<Thread::PLOT_1 priority=1 sleep>
ESPmoe:004:0->
{code}

!servosim-quickplot-1.png!
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision
# [25Jun2009]
# 02Jul2009 - no meeting; 4th of July break
# [09Jul2009]
# [16Jul2009]
# [23Jul2009]
# 30Jul2009 - Scott ran mtg; proposal preparation
# [06Aug2009]
# 13Aug2009 - cancelled; proposal/grant preparations
# [20Aug2009]
# 27Aug2009 - Jim Vacation; Scott in charge
# 03Sep2009 - Jim Vacation; Scott in charge
# [10Sep2009]
# 01Oct2009]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 28, 2008*

*11am-12*
Present: Doug, Chris S, SCott, Addie,

h3. Tech Transfer


h6. Discussion Items:

Update on Mack:

h3. MFB

Discussion Items:
* Weak pos on Mon, but nothing since. Found that reagents were dead. New reagents on the block now.
* LLNL replacing components on the new boards.
* April fecal water sample purification test.

h3. Software


h3. Sphere and 4K DWSMS

* Sphere update
** {color:#339999}No word or update from Wah Chang.{color}

* DWSM progress?
** {color:#339999}Doug believes he's found a pump that will push reliable, reproducible amounts of fluid.&nbsp; Ordering motor to run it, and now must test that it pushes the correct volumes of fluids with no back-flow.{color}
* Battery boxes?&nbsp; {color:#339999}IN{color}
* {color:#339999}Batteries oredered? Yes{color}

ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)
ACTION:&nbsp; New surface can lid discrepency, Jim was going to meet with Gene about it. (Jim)

h3. GUI Development

Image Handling processing: ]]></property>
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<property name="body"><![CDATA[These are some notes about the servo model design and implementation.

Here are some of the plots generated from the unit tests:

| !test_similar_to_servoTest.png!  |  !test_absMoves_with_direction_change_before_stop.png! | 
| !test_setRawLimits_and_abrupt_stop_overCurrent.png!  | !test_getTimesForLimits.png!    | 
| !test_CompositeFunction_simple.png!                       | 

h1. Design in a nutshell

At time of writing the code resides in the 'servomodel' branch:
   https://github.com/MBARI-ESP/ESP2Gscript/tree/servomodel

The main source file, where the {{I2C::Servo::Model}} class is defined is: [servomodel.rb|https://github.com/MBARI-ESP/ESP2Gscript/blob/b63f5de300c96e1d2e1f68f7ac13eab01fa3e7f5/lib/i2c/model/servomodel.rb].

The servo simulation is modularized in a layered way. Elements of the modeling itself are under the {{ServoModeling}} module:

- {{Servo::Model}} and related elements are only concerned, in terms of the characterization of the velocity-position function, with {{ServoChannelSimulator}}.

- {{ServoChannelSimulator}} makes use of a {{FunctionFactory}} to keep and adjust the overall velocity-position function according to move commands.

- {{FunctionFactory}} facilitates the construction of {{Function}}'s.

- Possible {{Function}}'s are:
-- {{ConstantFunction}}: function always evaluating to {{\[0, pos\]}} for a given position
-- {{MonotoneFunction}}: captures the basic velocity profile of starting at a given velocity, and then going through acceleration, plateau (each of which can be of zero duration), and deceleration zones. Starting at a given initial position, this function changes the position monotonically in a given direction.
-- {{CompositeFunction}}: function composed of the concatenation of multiple functions, each applied from a specific time wrt the previous one.


h1. Testing

h2. Unit tests

All unit tests can be run at the command line as follows:

{code}
$ find test/lib/i2c/model -name \*_test.rb -exec ruby -I. -Ilib -Iutils -Itest/lib {} \;
Loaded suite test/lib/i2c/model/servo/function_test
Started
..........
Finished in 0.013645 seconds.

10 tests, 607 assertions, 0 failures, 0 errors
Loaded suite test/lib/i2c/model/servo/functionfact_test
Started
..........
Finished in 0.029115 seconds.

10 tests, 1068 assertions, 0 failures, 0 errors
Loaded suite test/lib/i2c/model/servo/servochannelsim_test
Started
.......
Finished in 0.08877 seconds.

7 tests, 2531 assertions, 0 failures, 0 errors
Loaded suite test/lib/i2c/model/servomodel_test
Started
.......
Finished in 0.188708 seconds.

7 tests, 184 assertions, 0 failures, 0 errors
{code}

h2. Integration tests

{code}
carueda@bufflehead:~/esp2$ . bin/ESPenv shallow moe
carueda@bufflehead:~/esp2$ ESPmode=simfast
carueda@bufflehead:~/esp2$ esp
ESPmoe:001:0-> require 'plot'
true
ESPmoe:002:0-> ssLog = SS.log {SS.home.empty; SS.fill}
SS.reconfigure SSconfig
SS.home.seek empty
@16:00:00.82 SS.seek 25.00ml
[<I2C::Servo::Status enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=-12, velocity=-12, current=0, pwm=0, err=0, inPress=0, outPress=0, deltaPress=0, voltage=12.1620363279332>,
...
 <I2C::Servo::Status enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=108084, velocity=12, current=0, pwm=0, err=0, inPress=0, outPress=0, deltaPress=0, voltage=12.1620363279332>,
 <I2C::Servo::Status enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=108096, velocity=0, current=0, pwm=0, err=0, inPress=0, outPress=0, deltaPress=0, voltage=12.1620363279332>]
ESPmoe:003:0-> plot ssLog
#<Thread::PLOT_1 priority=1 sleep>
ESPmoe:004:0->
{code}

!servosim-quickplot-1.png!
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision
# [25Jun2009]
# 02Jul2009 -- no meeting; 4th of July break
# [09Jul2009]
# [16Jul2009]
# [23Jul2009]
# 30Jul2009 -- Scott ran mtg; proposal preparation
# [06Aug2009]
# 13Aug2009 -- cancelled; proposal/grant preparations
# [20Aug2009]
# 27Aug2009 -- Jim Vacation; Scott in charge
# 03Sep2009 -- Jim Vacation; Scott in charge
# [10Sep2009]]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 28, 2008*

*11am-12*
Present:


h3. Tech Transfer


h6. Discussion Items:


h3. MFB


h3. Software


h3. Sphere and 4K DWSMS


h3. GUI Development]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Feb 28, 2008*

*11am-12*
Present: Doug, Chris S, SCott, Addie,

h3. Tech Transfer


h6. Discussion Items:

Update on Mack:

h3. MFB

Discussion Items:
* Weak pos on Mon, but nothing since. Found that reagents were dead. New reagents on the block now.
* LLNL replacing components on the new boards.
* April fecal water sample purification test.

h3. Software


h3. Sphere and 4K DWSMS

* Sphere update
** {color:#339999}No word or update from Wah Chang.{color}

* DWSM progress?
** {color:#339999}Doug believes he's found a pump that will push reliable, reproducible amounts of fluid.&nbsp; Ordering motor to run it, and now must test that it pushes the correct volumes of fluids with no back-flow.{color}
* Battery boxes?&nbsp; {color:#339999}IN{color}
* {color:#339999}Batteries oredered? Yes{color}

ACTION:&nbsp; Have BATTERIES been ordered? Yes
ACTION:&nbsp; Change cracked power connector on GG's lid (Cheri)
ACTION:&nbsp; New surface can lid discrepency, Jim was going to meet with Gene about it. (Jim)

h3. GUI Development

Image Handling processing: ]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2019Feb08.pdf]
# [Engineering Timeline]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science]]></property>
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<property name="body"><![CDATA[h2. Overview

h2. Notes

The printer used by [~scholin] is a custom printer. It can not output GAL files. It does put out a text file that I'm trying to parse and work with. A copy of the file is checked into [SVN|http://kahuna.shore.mbari.org/viewvc.cgi/esp/trunk/esp-imaging/src/test/resources/imaging/2_22_08comptest_2008-02-25_142348_Run.txt?view=markup].

h3. Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:
{noformat}
SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK
{noformat}

SpotX and SpotY are coordinates in micrometers starting in the upper left hand corner of the paper. The _0, 0_ point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out

h4. References
# Old ESP Matlab toolbox at [http://moonjelly/cgi-bin/cvsweb.cgi/ESP/matlab/]
]]></property>
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<property name="body"><![CDATA[h2. Overview

h2. Notes

The printer used by [~scholin] is a custom printer. It can not output GAL files. It does put out a text file that I'm trying to parse and work with. A copy of the file is checked into [SVN|http://kahuna.shore.mbari.org/viewvc.cgi/esp/trunk/esp-imaging/src/test/resources/imaging/2_22_08comptest_2008-02-25_142348_Run.txt?view=markup].

h3. Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:
{noformat}
SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK
{noformat}

SpotX and SpotY are coordinates in micrometers starting in the upper left hand corner of the paper. The _0, 0_ point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">3179338</id>
<property name="body"><![CDATA[h2. Overview

h2. Notes

The printer used by [~scholin] is a custom printer. It can not output GAL files. It does put out a text file that I'm trying to parse and work with. A copy of the file is checked into [http://kahuna.shore.mbari.org/viewvc.cgi/esp/trunk/esp-imaging/src/test/resources/imaging/2_22_08comptest_2008-02-25_142348_Run.txt?view=markup|SVN].

h3. Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:
{noformat}
SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK
{noformat}

SpotX and SpotY are coordinates in micrometers starting in the upper left hand corner of the paper. The _0, 0_ point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out]]></property>
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<property name="body"><![CDATA[h2. Overview

h2. Notes

The printer used by [~scholin] is a custom printer. It can not output GAL files. It does put out a text file that I'm trying to parse and work with. A copy of the file is checked into SVN.

h3. Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:
{noformat}
SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK
{noformat}

SpotX and SpotY are coordinates in micrometers starting in the upper left hand corner of the paper. The _0, 0_ point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out]]></property>
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<property name="body"><![CDATA[h2. Overview

h2. Notes

h3. Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:
{noformat}
SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK
{noformat}

SpotX and SpotY are coordinates in micrometers starting in the upper left hand corner of the paper. The _0, 0_ point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out]]></property>
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<property name="body"><![CDATA[h2. For the developers

# [Getting the source|http://oceana/projects/esp/source-repository.html]
# [Opening in an IDE]
# [Scholin email - Things to track\- 07-Sep-2007|^ESPGUIDMthingstotrackextractfromlog.htm]]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Mar 6, 2008*

*10:00 am* Present: Pargett, Jensen, Marin, Everlove.

h3. Tech Transfer


h6. Discussion Items:

Mock fridge mission, 3/12 to 3/19

Loading and QC of reagents on Monday. Puck loading on Monday.&nbsp;Mack going into the fridge on Tuesday.

Still need ISUS, have CTD, need to be batteried and programmed.

Scott will test GPS tracking outside, won't be active during mock mission.\\

h3. MFB

Not discussed.

h3. Software

Not discussed

h3. Sphere and 4K DWSMS

Torque testing shows we can get the LVLP pump on a dwarf, the HVLP will be marginal, and the LVHP will need a seperate amop. Scott is working on that arrangment.

h3. GUI Development

Not discussed]]></property>
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<property name="creatorName"><![CDATA[kgomes]]></property>
<property name="creationDate">2007-04-03 14:00:45.247</property>
<property name="lastModifierName"><![CDATA[kgomes]]></property>
<property name="lastModificationDate">2007-10-24 10:09:26.637</property>
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<property name="body"><![CDATA[Priority, What we need, (number).&nbsp;

Black \--> we do in house, {color:#0000ff}Blue \--> can be sent out (Mike decides){color}
* 1, Mushroom caps - 1003526-004 \-(20) {color:#ff0000}\- Mike has made (5) and will send the rest out for quote (1/31/08){color}
* -1, Bulkhead V. mounting brackets - P-200325-07 - (6)- {color:#ff0000}(02/04/08){color}
* -1, Plate Caps (2)- {color:#ff0000}\- (1/31/08){color}
* 1-Mike, {color:#0000ff}Waste Container - 1003526-001 - (2){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08) PO #0810307 -{color} {color:#000000}Rcvd 3/3/08{color}
* 1-Mike, {color:#0000ff}Waste container supports - 1003526-003 - (6){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08) PO #0810307 -{color} {color:#000000}Rcvd 3/3/08{color}
* 1-Mike, {color:#0000ff}Bag Hanger Assemblies - 1003523-01-02-03 - (5){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08) PO #0810307 -{color} {color:#000000}Rcvd 3/3/08{color}

| {color:#009900}Bag Assembly Parts&nbsp;{color} | {color:#009900}For 5 Instruments{color} | {color:#009900}We currently have{color} | {color:#009900}We thus need (minimum){color} |
| -Hoops- | 10L&nbsp; 5mL&nbsp; 15sm \\ | 4L&nbsp; 1mL&nbsp; 2sm \\ | -6L&nbsp; 4mL&nbsp; 13sm- {color:#ff0000}(02/11/08){color} \\ |
| Crescent Closet Bar \\ | 7 | 3 | 4 {color:#ff0000}Rcvd 3/3/08{color} |
| Bushing Assemb 4/instrument \\ | 20 | 14 | -6- {color:#ff0000}None Needed{color} |
* 2, Modem Battery cylinder - 10020051-01 - (1)
* 2, {color:#0000ff}Sample ports - 1002516 - (4){color} {color:#ff0000}(2/19/08){color}
* 2, spin can zinc down (3)
* 2, can-side CTD bracket (2)
* 2, {color:#0000ff}sample intake copper screen holder - 1002516-02 - (4){color}
* 2, bail locking plates (4)
* 2, adaptor plate for mooring (2)
* -3, CTV mount - 1002330-019 - (3)- {color:#ff0000}(2/04/08){color}
* -3, forearm motor shaft adaptor - 1002451-006 - (2)- {color:#ff0000}(02/05/08){color}
* -3, finger motor shaft adaptor - 1002451-006 short - (2)- {color:#ff0000}(02/05/08){color}
* -3, slot the encoder shafts (8)- {color:#ff0000}(02/11/08){color}
* {color:#ff0000}3 Parker Pucker Un-Stuckers - Solids and Prints ready (02/12/08){color}]]></property>
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<property name="body"><![CDATA[# [2008 Q1-Q2 Schedule (rev 1)]
# [2008 Q1-Q2 Schedule (rev 2)]
# [2008 Q1-Q2 Schedule (rev 3)]
# [2008 Q1-Q2 Schedule (rev 4)]
# [2008 Q1-Q2 Schedule (rev 5)]
# [Machinist build schedule (Feb 2007)]]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Jan 31, 2008*

*11am-12*
Present: Jim, Chris S., Kevin, Doug, Cheri, Brent, Scott, Addie
\\

h3. Tech Transfer


h6. Discussion Items:

* Results of hand/arm testing.&nbsp;&nbsp;
** {color:#339999}Mack has been cold-tested and Brent is working on temp sensor testing.{color}
** {color:#339999}Bruce--all valves are in, hand mostly assembled, still to finish plumbing{color}
* Mike Parker Machining [list|ESPAPP:Machinist build schedule (Feb 2007)] \-\- working quickly through it
* New hand order.&nbsp; Plans update?&nbsp; Mike ready to go to El Camino?&nbsp; How many?&nbsp; {color:#339999}N{color}
** {color:#339999}New hands to be ordered this summer.&nbsp; XX hand assemblies + 3 sets of fingers with new fulcrum positions to replace the existing 'new' fingers{color}
* New syringe cost.&nbsp;
** {color:#339999}Still not heard back from company{color}
* New Dwarf Boards.&nbsp; \~$4K/system with 6 week lead time.&nbsp; Account?&nbsp; How many?&nbsp;
** {color:#339999}Jose still forming the database.&nbsp; Just a core, but all electronics (no MFB),&nbsp; Jose should charge 900612,&nbsp; maybe a subaccount (.99 for CIP)).{color}

+Action Items+\\
\\

+Action Items from last week:+

ACTION: check with Jose about number of dwarves to order (Scott)&nbsp; {color:#ff0000}In progress:{color}&nbsp; Jose has mad the first pass through and looks like all components are still available.&nbsp; Jose getting price and lead time on everything.

ACTION:&nbsp; syringes.&nbsp; Wait to hear from company final costs and order #'s and get sample of their new product. (Scott)&nbsp; {color:#ff0000}In progress&nbsp;{color}

ACTION:&nbsp; Will cast a new schedule taking into account our current progress (Jim/Cheri/Scott)&nbsp; {color:#0000ff}Finished{color}
ACTION:&nbsp; Order fluidic fittings for cores and MFB (Cheri)&nbsp; {color:#0000ff}Finished{color}
ACTION: Will drill out pressure sensor holes in clamps when we revalve the cores. (Scott/Cheri)&nbsp; {color:#0000ff}Finished{color}

h3. MFB

Discussion Items:
* Getting excellent yields out of solid-phase-extraction--Good job Addie and Chris P\!\!
* Mixing column basically finished
* next week will make extract from seawater lysate and compare to bench-top
* in parallel, do dye tests with heater block.

ACTION:&nbsp; Hook up heater block and test diodes for fluorescence sensitivity. (Addie)&nbsp; {color:#ff0000}In progress{color}
ACTION: Will work on figuring cable problem to three-way valves. (Addie) {color:#0000ff}Finished{color}
ACTION: Mike will bore out stator on the mixing column so we don't need more mix tubing or reducing fittings. (Addie) {color:#0000ff}Finished{color}
ACTION: Fan not working on PCR module and Addie will try and track down why (check in various terminal/call LLNL) bob said he's never had the fan turn on or off with that module. (Addie); {color:#0000ff}Finished{color}

h3. Software

* puck heating control
** now can send a temperature to puck and it gets there in 2-3 minutes with little overshoot
* Brent would like to pull calibration values out into a structure, since they are different on each instrument

+Action Items:+&nbsp;

ACTION:&nbsp; Finish by Feb 6 the temperature calibration model, incorporating Scott's prior work if possible. (Brent)
ACTION:&nbsp; make another temperature puck (Scott)
ACTION:&nbsp; Write 'cheat sheet' showing new parameter available for changing during sample collection (Brent)

+Action Items from last week:+

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)&nbsp; {color:#ff0000}In progress:{color} Can't find elmo but have other pieces.
ACTION:&nbsp; working on a cue of interrupts in the threading environment (Brent): {color:#ff0000}Low priority Not started{color}
ACTION:&nbsp; Work with the auto-cal code for carosal and aligment (Brent):&nbsp; {color:#ff0000}Medium priority Not started{color}

h3. Sphere and 4K DWSMS

* Screen drawings.&nbsp;

Battery boxes?&nbsp; {color:#339999}Scott still waiting to hear.{color}
* DWSM progress?&nbsp;&nbsp; {color:#339999}Have \~$1300 of parts coming into lab to build lung system.&nbsp; Going into Bldg B lab.&nbsp; pumps not coming in yet, but will find hand-pumps.&nbsp; Will start construction next week.&nbsp; Maybe need some days of Jim S.{color}

{color:#000000}ACTION:{color}&nbsp; Waiting for company to return yes/no on whether they can manufacture screens to mass instead of size. (Doug/Scott)&nbsp; {color:#ff0000}In progress{color}
ACTION:&nbsp; Order two battery boxes (w/out batteries)--~$4K; account #701312.04: {color:#ff0000}In progress{color}:&nbsp; Scott waiting for lower price

ACTION:&nbsp; Go back to Mark Brown and ask who we should go with (Jim): {color:#0000ff}Finished{color} (Tapemation is it unless we want to go back east)&nbsp;

h3. &nbsp;


h3. GUI Development

* Mission script GUI introduction

Kevin showed how to use the mission script GUI located [here|http://predator.shore.mbari.org/esp_gui/launch.jnlp].
Bugs for this GUI can be reported [here|http://oceana.shore.mbari.org:8082].&nbsp;
\\
\\

*On Table:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)]]></property>
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<property name="body"><![CDATA[h1. *ESP Engineering Mtg \-\-* *Mar 6, 2008*

*11am-12*
Present:

h3. Tech Transfer


h6. Discussion Items:


h3. MFB


h3. Software


h3. Sphere and 4K DWSMS


h3. GUI Development]]></property>
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<property name="body"><![CDATA[Priority, What we need, (number).&nbsp;

Black \--> we do in house, {color:#0000ff}Blue \--> can be sent out (Mike decides){color}
* 1, Mushroom caps - 1003526-004 \-(20) {color:#ff0000}\- Mike has made (5) and will send the rest out for quote (1/31/08){color}
* -1, Bulkhead V. mounting brackets - P-200325-07 - (6)- {color:#ff0000}(02/04/08){color}
* -1, Plate Caps (2)- {color:#ff0000}\- (1/31/08){color}
* 1-Mike, {color:#0000ff}Waste Container - 1003526-001 - (2){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08) PO #0810307{color}
* 1-Mike, {color:#0000ff}Waste container supports - 1003526-003 - (6){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08) PO #0810307{color}
* 1-Mike, {color:#0000ff}Bag Hanger Assemblies - 1003523-01-02-03 - (5){color} {color:#ff0000}\- Mike has sent prints out for bid (1/31/08) PO #0810307{color}

| {color:#009900}Bag Assembly Parts&nbsp;{color} | {color:#009900}For 5 Instruments{color} | {color:#009900}We currently have{color} | {color:#009900}We thus need (minimum){color} |
| -Hoops- | 10L&nbsp; 5mL&nbsp; 15sm \\ | 4L&nbsp; 1mL&nbsp; 2sm \\ | -6L&nbsp; 4mL&nbsp; 13sm- {color:#ff0000}(02/11/08){color} \\ |
| Crescent Closet Bar \\ | 7 | 3 | 4 {color:#ff0000}Sent Out{color} |
| Bushing Assemb 4/instrument \\ | 20 | 14 | -6- {color:#ff0000}None Needed{color} |
* 2, Modem Battery cylinder - 10020051-01 - (1)
* 2, {color:#0000ff}Sample ports - 1002516 - (4){color}
* 2, spin can zinc down (3)
* 2, can-side CTD bracket (2)
* 2, {color:#0000ff}sample intake copper screen holder - 1002516-02 - (4){color}
* 2, bail locking plates (4)
* 2, adaptor plate for mooring (2)
* -3, CTV mount - 1002330-019 - (3)- {color:#ff0000}(2/04/08){color}
* -3, forearm motor shaft adaptor - 1002451-006 - (2)- {color:#ff0000}(02/05/08){color}
* -3, finger motor shaft adaptor - 1002451-006 short - (2)- {color:#ff0000}(02/05/08){color}
* -3, slot the encoder shafts (8)- {color:#ff0000}(02/11/08){color}
* {color:#ff0000}3 Parker Pucker Un-Stuckers - Solids and Prints ready (02/12/08){color}]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab'. NOTE: The color selector was used in an older version to display on the calendar but is no longer used and will be removed in the future, you can ignore the color chooser.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|align=centre!
# I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the ESP and Mission Tabs Window.  If you click on the "ESP" table you will see a short table with the information about the ESP that is running the mission you are examining (in this case, Gordon).
!ESPGUIFigure19.jpg|align=centre!
If you select the "Planned" tab, you will see a tabular view of the various protocols that you defined in the mission planning phase.
!ESPGUIFigure20.jpg|thumbnail,align=centre!
You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Samples", "Images" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates.  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the file are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take awhile to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
Figure 23
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
Figure 24.
A window will open showing you the progress of the log file parsing.
Figure 25
Log file during parsing
Figure 26
Log file parsing complete.
]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab'. NOTE: The color selector was used in an older version to display on the calendar but is no longer used and will be removed in the future, you can ignore the color chooser.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse over the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|align=centre!
# I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the ESP and Mission Tabs Window.  If you click on the "ESP" table you will see a short table with the information about the ESP that is running the mission you are examining (in this case, Gordon).
!ESPGUIFigure19.jpg|align=centre!
If you select the "Planned" tab, you will see a tabular view of the various protocols that you defined in the mission planning phase.
!ESPGUIFigure20.jpg|thumbnail,align=centre!
You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Samples", "Images" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates.  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the file are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take awhile to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
Figure 23
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
Figure 24.
A window will open showing you the progress of the log file parsing.
Figure 25
Log file during parsing
Figure 26
Log file parsing complete.
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|thumbnail,align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|thumbnail,align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|thumbnail,align=centre!
# I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|thumbnail,align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|thumbnail,align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the ESP and Mission Tabs Window.  If you click on the "ESP" table you will see a short table with the information about the ESP that is running the mission you are examining (in this case, Gordon).
!ESPGUIFigure19.jpg|thumbnail,align=centre!
If you select the "Planned" tab, you will see a tabular view of the various protocols that you defined in the mission planning phase.
!ESPGUIFigure20.jpg|thumbnail,align=centre!
You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Samples", "Images" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates.  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|thumbnail,align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the file are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take awhile to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
Figure 23
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
Figure 24.
A window will open showing you the progress of the log file parsing.
Figure 25
Log file during parsing
Figure 26
Log file parsing complete.
]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab'. NOTE: The color selector was used in an older version to display on the calendar but is no longer used and will be removed in the future, you can ignore the color chooser.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|thumbnail,align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|thumbnail,align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|thumbnail,align=centre!
# I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|thumbnail,align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|thumbnail,align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the ESP and Mission Tabs Window.  If you click on the "ESP" table you will see a short table with the information about the ESP that is running the mission you are examining (in this case, Gordon).
!ESPGUIFigure19.jpg|thumbnail,align=centre!
If you select the "Planned" tab, you will see a tabular view of the various protocols that you defined in the mission planning phase.
!ESPGUIFigure20.jpg|thumbnail,align=centre!
You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Samples", "Images" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates.  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|thumbnail,align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the file are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take awhile to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
Figure 23
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
Figure 24.
A window will open showing you the progress of the log file parsing.
Figure 25
Log file during parsing
Figure 26
Log file parsing complete.
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab'. NOTE: The color selector was used in an older version to display on the calendar but is no longer used and will be removed in the future, you can ignore the color chooser.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse over the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For this reason, we don't allow spaces in mission names.  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/15/2011 00:00:00 |
| End Date | The date at which the mission will end | 8/31/2011 00:00:00 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | ftp.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://ftp.mbari.org/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_ which means the host is _ftp.mbari.org_ and the FTP Root is _/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|align=centre!
# What you now see is a small calendar icon in the upper portion of the colored mission bar on the calendar.  It is place at the top of the mission bar to indicate that it is a planned protocol, not one that was extracted from the log file (which you will see later).  Also, the small pencil on the icon means that it is a planned protocol, not an actual one.  The small letter at the front of the icon is used to help distinguish the which protocol this is.  It is simply the first letter of the name that you gave the protocol.  You will alos notice the list of "Planned" protocols in the lower left pane shows the list of protocols you have planned so far.  I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the Protocol, Event and Data Window.  As mentioned above, the first tab "Planned" shows you the protocols that have been planned for this mission (what you created earlier). You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Images", "Errors" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates (which we will do shortly).  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the file are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take awhile to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
Figure 23
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
Figure 24.
A window will open showing you the progress of the log file parsing.
Figure 25
Log file during parsing
Figure 26
Log file parsing complete.
]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab'. NOTE: The color selector was used in an older version to display on the calendar but is no longer used and will be removed in the future, you can ignore the color chooser.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse over the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For this reason, we don't allow spaces in mission names.  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/15/2011 00:00:00 |
| End Date | The date at which the mission will end | 8/31/2011 00:00:00 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | ftp.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://ftp.mbari.org/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_ which means the host is _ftp.mbari.org_ and the FTP Root is _/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|align=centre!
# What you now see is a small calendar icon in the upper portion of the colored mission bar on the calendar.  It is place at the top of the mission bar to indicate that it is a planned protocol, not one that was extracted from the log file (which you will see later).  Also, the small pencil on the icon means that it is a planned protocol, not an actual one.  The small letter at the front of the icon is used to help distinguish the which protocol this is.  It is simply the first letter of the name that you gave the protocol.  You will alos notice the list of "Planned" protocols in the lower left pane shows the list of protocols you have planned so far.  I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the Protocol, Event and Data Window.  As mentioned above, the first tab "Planned" shows you the protocols that have been planned for this mission (what you created earlier). You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Images", "Errors" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates (which we will do shortly).  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the files are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take a while to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
Figure 23
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
Figure 24.
A window will open showing you the progress of the log file parsing.
Figure 25
Log file during parsing
Figure 26
Log file parsing complete.
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab'. NOTE: The color selector was used in an older version to display on the calendar but is no longer used and will be removed in the future, you can ignore the color chooser.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse over the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For this reason, we don't allow spaces in mission names.  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/15/2011 00:00:00 |
| End Date | The date at which the mission will end | 8/31/2011 00:00:00 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | ftp.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://ftp.mbari.org/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_ which means the host is _ftp.mbari.org_ and the FTP Root is _/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|align=centre!
# I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the ESP and Mission Tabs Window.  If you click on the "ESP" table you will see a short table with the information about the ESP that is running the mission you are examining (in this case, Gordon).
!ESPGUIFigure19.jpg|align=centre!
If you select the "Planned" tab, you will see a tabular view of the various protocols that you defined in the mission planning phase.
!ESPGUIFigure20.jpg|thumbnail,align=centre!
You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Samples", "Images" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates.  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the file are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take awhile to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
Figure 23
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
Figure 24.
A window will open showing you the progress of the log file parsing.
Figure 25
Log file during parsing
Figure 26
Log file parsing complete.
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab'. NOTE: The color selector was used in an older version to display on the calendar but is no longer used and will be removed in the future, you can ignore the color chooser.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse over the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For this reason, we don't allow spaces in mission names.  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/15/2011 00:00:00 |
| End Date | The date at which the mission will end | 8/31/2011 00:00:00 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | ftp.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://ftp.mbari.org/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_ which means the host is _ftp.mbari.org_ and the FTP Root is _/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|align=centre!
# What you now see is a small calendar icon in the upper portion of the colored mission bar on the calendar.  It is place at the top of the mission bar to indicate that it is a planned protocol, not one that was extracted from the log file (which you will see later).  Also, the small pencil on the icon means that it is a planned protocol, not an actual one.  The small letter at the front of the icon is used to help distinguish the which protocol this is.  It is simply the first letter of the name that you gave the protocol.  You will alos notice the list of "Planned" protocols in the lower left pane shows the list of protocols you have planned so far.  I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the ESP and Mission Tabs Window.  If you click on the "ESP" table you will see a short table with the information about the ESP that is running the mission you are examining (in this case, Gordon).
!ESPGUIFigure19.jpg|align=centre!
If you select the "Planned" tab, you will see a tabular view of the various protocols that you defined in the mission planning phase.
!ESPGUIFigure20.jpg|thumbnail,align=centre!
You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Samples", "Images" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates.  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the file are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take awhile to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
Figure 23
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
Figure 24.
A window will open showing you the progress of the log file parsing.
Figure 25
Log file during parsing
Figure 26
Log file parsing complete.
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|thumbnail,align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|thumbnail,align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|thumbnail,align=centre!
# I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|thumbnail,align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|thumbnail,align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the ESP and Mission Tabs Window.  If you click on the "ESP" table you will see a short table with the information about the ESP that is running the mission you are examining (in this case, Gordon).
!ESPGUIFigure19.jpg|thumbnail,align=centre!
If you select the "Planned" tab, you will see a tabular view of the various protocols that you defined in the mission planning phase.
!ESPGUIFigure20.jpg|thumbnail,align=centre!
You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Samples", "Images" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates.  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|thumbnail,align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the file are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take awhile to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
Figure 23
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
Figure 24.
A window will open showing you the progress of the log file parsing.
Figure 25
Log file during parsing
Figure 26
Log file parsing complete.
]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|thumbnail,align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|thumbnail,align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|thumbnail,align=centre!
# I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|thumbnail,align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|thumbnail,align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the ESP and Mission Tabs Window.  If you click on the "ESP" table you will see a short table with the information about the ESP that is running the mission you are examining (in this case, Gordon).
!ESPGUIFigure19.jpg|thumbnail,align=centre!
If you select the "Planned" tab, you will see a tabular view of the various protocols that you defined in the mission planning phase.
!ESPGUIFigure20.jpg|thumbnail,align=centre!
You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Samples", "Images" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates.  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|thumbnail,align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the file are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take awhile to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
Figure 23
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
Figure 24.
A window will open showing you the progress of the log file parsing.
Figure 25
Log file during parsing
Figure 26
Log file parsing complete.
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|thumbnail,align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|thumbnail,align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|thumbnail,align=centre!
# I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|thumbnail,align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|thumbnail,align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the ESP and Mission Tabs Window.  If you click on the "ESP" table you will see a short table with the information about the ESP that is running the mission you are examining (in this case, Gordon).
!ESPGUIFigure19.jpg|thumbnail,align=centre!
If you select the "Planned" tab, you will see a tabular view of the various protocols that you defined in the mission planning phase.
!ESPGUIFigure20.jpg|thumbnail,align=centre!
You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Samples", "Images" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates.  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|thumbnail,align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the file are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take awhile to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
Figure 23
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
Figure 24.
A window will open showing you the progress of the log file parsing.
Figure 25
Log file during parsing
Figure 26
Log file parsing complete.
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<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically (colors are same deployment)+

{color:#ff00ff}April 6--Bruce at M0 for surface deployment (Zephyr){color}

April 15--Mack in Sphere (dive #1) for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in Sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

{color:#ff00ff}April 29--Recover Bruce at M0 (Zephyr){color}

May 1--Mack in Sphere (dive #3) connected to DWSM; incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

{color:#0033cc}May 14--Deploy NEO w/PCR, surface deployment (Zephyr){color}

May 27--First Drifter dive; used weighted cable (Zephyr)

June 5-9 \-\- Western Flyer Trip.&nbsp; D-ESP, Drifter, and CTD casts. {color:#cc0000}{*}MOVIES{*}{color}:  D-ESP launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/DESP%20deployment%20(full%20quality).dv].  Drifter launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/Drifter.dv].

{color:#0033cc}June 11 \-\- Recover NEO.&nbsp; (Zephyr){color}\\

+FALL Network Deployment+

Proposed locations are here: [http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&msid=113879459163411006053.000471828af997bd7d89c&t=h&z=12]

{color:#ff6600}September 24 \-\- Deploy Moe w/PCR at M0.&nbsp; Deployed Mack at Santa Cruz{color}.&nbsp; {color:#66cc00}Deployed Bruce in the bight.&nbsp; (Zephyr)&nbsp; Lost communications with Bruce that day.{color}

{color:#66cc00}September 28 \-\- Recover (dead) Bruce.&nbsp; Comms box had water in it, but radio worked.&nbsp; EM cable had 2 broken wires. (Zephyr){color}

{color:#cc0000}September 30 \-\- Deploy D-ESP on MARS (Lobos).{color}&nbsp; Hand issue at first, but 'fixed' itself.&nbsp; Worked until Oct. 7 when wrong puck was loaded and water introduced into core, frying puck heater.&nbsp; We turned off and first recovery day (Oct 13) is weathered out.&nbsp; It still awaits recovery.

{color:#66cc00}October 14 \-\- Re-deploy Bruce (Zephyr).&nbsp; New comms box, re-terminated EM cable.&nbsp; Working well after deployment.{color}

October 20 \-\- Install pump system on pier at Santa Cruz Wharf. October 22 \-\- Neo installed on SC Wharf.

{color:#cc0000}October 30 \-\- Recover D-ESP off MARS (Lobos).{color}

{color:#ff6600}October 29 \-\- Recover both Moe from M0 and Mack from Santa Cruz (Zephyr).{color}

{color:#66cc00}November 2 \-\- Recover Bruce from the bight (Zephyr).&nbsp; This ends Fall Network Deployment.{color}

November 25 \-\- Recover NEO from SC Wharf.]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|thumbnail,align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|thumbnail,align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|thumbnail,align=centre!
# I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|thumbnail,align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|thumbnail,align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the ESP and Mission Tabs Window.  If you click on the "ESP" table you will see a short table with the information about the ESP that is running the mission you are examining (in this case, Gordon).
!ESPGUIFigure19.jpg|thumbnail,align=centre!
If you select the "Planned" tab, you will see a tabular view of the various protocols that you defined in the mission planning phase.
!ESPGUIFigure20.jpg|thumbnail,align=centre!
You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Samples", "Images" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates.  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|thumbnail,align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the file are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take awhile to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
Figure 23
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
Figure 24.
A window will open showing you the progress of the log file parsing.
Figure 25
Log file during parsing
Figure 26
Log file parsing complete.
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are four main areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "ESP and Mission Tabs Window" (lower left corner)
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|thumbnail,align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|thumbnail,align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|thumbnail,align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|thumbnail,align=centre!
# I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|thumbnail,align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|thumbnail,align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the ESP and Mission Tabs Window.  If you click on the "ESP" table you will see a short table with the information about the ESP that is running the mission you are examining (in this case, Gordon).
!ESPGUIFigure19.jpg|thumbnail,align=centre!
If you select the "Planned" tab, you will see a tabular view of the various protocols that you defined in the mission planning phase.
!ESPGUIFigure20.jpg|thumbnail,align=centre!
You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Samples", "Images" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates.  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|thumbnail,align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the file are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take awhile to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
Figure 23
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
Figure 24.
A window will open showing you the progress of the log file parsing.
Figure 25
Log file during parsing
Figure 26
Log file parsing complete.
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<id name="id">18285262</id>
<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|thumbnail,align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|thumbnail,align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|thumbnail,align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|thumbnail,align=centre!
# I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|thumbnail,align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|thumbnail,align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the ESP and Mission Tabs Window.  If you click on the "ESP" table you will see a short table with the information about the ESP that is running the mission you are examining (in this case, Gordon).
!ESPGUIFigure19.jpg|thumbnail,align=centre!
If you select the "Planned" tab, you will see a tabular view of the various protocols that you defined in the mission planning phase.
!ESPGUIFigure20.jpg|thumbnail,align=centre!
You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Samples", "Images" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates.  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|thumbnail,align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the file are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take awhile to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
Figure 23
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
Figure 24.
A window will open showing you the progress of the log file parsing.
Figure 25
Log file during parsing
Figure 26
Log file parsing complete.
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<property name="body"><![CDATA[Our first 'labeled' scintered frits arrived *{+}23 April, 2008{+}*.&nbsp; These were 10um frits, labeled 'D'. Specifics of this order:

Job #36366
Disc Dimensions: 0.998 \+0.000/-0.002" OD x 0.062 \+/-0.005" thick
Porous Grade: 10 Micron Grade
No Chamfers
Porous material Chemistry: Titanium Grade 2 per unified
PO# 0810358&nbsp;

These frits did {color:#cc0000}NOT{color} have finished edges, and were 0.057" in thickness, within tolerance specified, but thinner than original frits.
Future orders should specify edging and a lower thickness tolerance to get closer to the 0.062" thickness.
\\

The convention, decided in emails Feb 26, 2008, will be:

0.1, 0.5, 1, 10um frits will be labeled

A, B, C, D respectively.&nbsp;
\\

We have had CE Metallurgical make the 'press' for these so subsequent batches should be less expensive.&nbsp;

*{+}March 26, 2009{+}*


Jobs #38015, 38016, 38017
Disc Dimensions: 0.998 \+0.000/-0.002 OD x 0.063 \+/-0.003" thick&nbsp; (note slightly thicker with narrower tolerance than first order)
PO# 0910403

0.1 um (labeld 'A') $10.25/ea
20.0 um (labeled 'E') $7.55/ea
50.0 um (labeled 'F') $7.55/ea

Ordered 100 of each size.


{color:#0000ff}Contact{color}:

Chand Eisenmann Metallurgical
258 Spielman Hwy
Burlington, CT&nbsp; 06013

860-675-5000

{color:#0000ff}email:{color}
me@chandeisenmann.com&nbsp; (Mark)]]></property>
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<property name="body"><![CDATA[Our first 'labeled' scintered frits arrived *{+}23 April, 2008{+}*.&nbsp; These were 10um frits, labeled 'D'. Specifics of this order:

Job #36366
Disc Dimensions: 0.998 \+0.000/-0.002" OD x 0.062 \+/-0.005" thick
Porous Grade: 10 Micron Grade
No Chamfers
Porous material Chemistry: Titanium Grade 2 per unified
PO# 0810358&nbsp;

These frits did {color:#cc0000}NOT{color} have finished edges, and were 0.057" in thickness, within tolerance specified, but thinner than original frits.
Future orders should specify edging and a lower thickness tolerance to get closer to the 0.062" thickness.
\\

The convention, decided in emails Feb 26, 2008, will be:

0.1, 0.5, 1, 10um frits will be labeled

A, B, C, D respectively.&nbsp;
\\

We have had CE Metallurgical make the 'press' for these so subsequent batches should be less expensive.&nbsp;

*{+}March 26, 2009{+}*

Jobs #38015, 38016, 38017
Disc Dimensions: 0.998 \+0.000/-0.002 OD x 0.063 \+/-0.003" thick&nbsp; (note slightly thicker with narrower tolerance than first order)
PO# 0910403

0.1 um (labeld 'A') $10.25/ea
20.0 um (labeled 'E') $7.55/ea
50.0 um (labeled 'F') $7.55/ea

Ordered 100 of each size.

*+&nbsp;December 30, 2009{+}*

Placed the following order:


Jobs
Disc Dimensions: 0.998 \+0.000/-0.002 OD x 0.063 \+/-0.003" thick
PO

0.2 um (100; labeled '2') $10.25/ea
0.5 um (100; labeled 'B') $10.25/ea
1.0 um (100; labeled 'C') $10.25/ea
10 um (300; labeled 'D') $5.85/ea

{color:#0000ff}Contact{color}:

Chand Eisenmann Metallurgical
258 Spielman Hwy
Burlington, CT&nbsp; 06013

860-675-5000

{color:#0000ff}email:{color}
me@chandeisenmann.com&nbsp; (Mark)]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab'. NOTE: The color selector was used in an older version to display on the calendar but is no longer used and will be removed in the future, you can ignore the color chooser.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse over the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For this reason, we don't allow spaces in mission names.  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/15/2011 00:00:00 |
| End Date | The date at which the mission will end | 8/31/2011 00:00:00 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | ftp.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://ftp.mbari.org/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_ which means the host is _ftp.mbari.org_ and the FTP Root is _/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|align=centre!
# What you now see is a small calendar icon in the upper portion of the colored mission bar on the calendar.  It is place at the top of the mission bar to indicate that it is a planned protocol, not one that was extracted from the log file (which you will see later).  Also, the small pencil on the icon means that it is a planned protocol, not an actual one.  The small letter at the front of the icon is used to help distinguish the which protocol this is.  It is simply the first letter of the name that you gave the protocol.  You will alos notice the list of "Planned" protocols in the lower left pane shows the list of protocols you have planned so far.  I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the Protocol, Event and Data Window.  As mentioned above, the first tab "Planned" shows you the protocols that have been planned for this mission (what you created earlier). You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Images", "Errors" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates (which we will do shortly).  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the files are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take a while to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
!ESPGUIFigure23.jpg|align=centre!
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
!ESPGUIFigure24.jpg|align=centre!
A window will open showing you the progress of the log file parsing.
!ESPGUIFigure25.jpg|align=centre!
Once the log interpretation is complete, you should see many more things in the calendar view.  In the figure below you will notice several new things.  The exclamation points in the middle of the mission bar on the calendar indicate an error during the run of the ESP and the calendar icons with green arrows at the bottom of the mission bar indicate protocols that were found in the log file.
!ESPGUIFigure26.jpg|align=centre!
At this point, we can begin to explore some information about the currently deployed ESP.  If you select the "Actual" tab in the lower left pane, you will see the list of protocols that were interpreted from the log file.  You see the name of the protocol, the start date and time, the target/actual volumes of the associated water sample and the difference between the target and actual (if there is one).
!ESPGUIFigure27.jpg|align=centre!
If you click on the protocol either in the calendar view or in the "Actual" table, you will see more details about the protocol in both the Protocol Graph Window and in the Context Sensitive Details Window.  In the following figure, I selected the first pcr protocol.
!ESPGUIFigure28.jpg|align=centre!
In the Protocol Graph Window you can see some details about the various related artifacts.  In this example, since this if from the Deep ESP, you can see that the water sample associated with the PCR itself was extracted from a DWSM sample.  You can also see the associated images that were taken of the analyzed sample associated with the PCR.  The WCR that is show gives you the information that there was indeed an archive performed in association with this PCR. In the context sensitive details window on the lower right side of the screen you can see the entry in the log file that the PCR protocol was extracted from.  If you select one of the images in the graph or switch to the "Images" tab, you will get more information about the image you have selected.
!ESPGUIFigure29.jpg|align=centre!
The image tab shows a table with some information about the selected image such as the date and time it was taken and the exposure that was used.  In the context sensitive details panel, you can see the image itself and if you select the "Metadata" tab you will see the information extracted from the TIFF image itself.  The "Log Entry" tab shows the location in the log file that this entry was extracted from.  Next if you select an Error exclamation point in the calendar view, or switch to the "Error" tab, you will get more information about the errors that were discovered in the log file.
!ESPGUIFigure30.jpg|align=centre!
In this example, you can see the error is the abort of the mission and when that error occurred.  In the context details window, you can see the log entry with a window of lines on both sides of the entry so you can see the context in which the error occurred. If you select the "Ancillary" tab, you can get information about the ancillary data that was extracted from the log file.  This is the data the is logged by sensors in the ESP itself in addition to other contextual sensors that are attached to the ESP and are logging their data through the ESP. In the example shown below, there is data available from the ESP Can itself as well as from an associated CTD and an ISUS.  If you select an appropriate time window (for this example, I chose Jul 17 through July 20, then choose the variables you are interested in and click "Refresh", you will see a plot of the various data in the context sensitive details window.
!ESPGUIFigure31.jpg|align=centre!
If you right-click on the plot itself, you will be presented with some options to save, print or zoom/pan the ancillary data plots.  
!ESPGUIFigure32.jpg|align=centre!
If you want to save the data that you have plotted, in the left window, click on the "Save Selected" button and it will present you with a file dialog so you can save a comma separated list of data points to your disk somewhere for further analysis. Note that in the resulting CSV file, the dates and times of the different data do not align and so where there is not data "N/A"s are inserted as excel understands those as no data.
]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]<--\-{color:#ff0000}{*}NEW (Oct 7, 2009{*}{color})
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [Functional Requirements for Gen 3 ESP]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab'. NOTE: The color selector was used in an older version to display on the calendar but is no longer used and will be removed in the future, you can ignore the color chooser.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse over the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For this reason, we don't allow spaces in mission names.  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/15/2011 00:00:00 |
| End Date | The date at which the mission will end | 8/31/2011 00:00:00 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | ftp.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://ftp.mbari.org/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_ which means the host is _ftp.mbari.org_ and the FTP Root is _/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|align=centre!
# What you now see is a small calendar icon in the upper portion of the colored mission bar on the calendar.  It is place at the top of the mission bar to indicate that it is a planned protocol, not one that was extracted from the log file (which you will see later).  Also, the small pencil on the icon means that it is a planned protocol, not an actual one.  The small letter at the front of the icon is used to help distinguish the which protocol this is.  It is simply the first letter of the name that you gave the protocol.  You will alos notice the list of "Planned" protocols in the lower left pane shows the list of protocols you have planned so far.  I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the Protocol, Event and Data Window.  As mentioned above, the first tab "Planned" shows you the protocols that have been planned for this mission (what you created earlier). You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Images", "Errors" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates (which we will do shortly).  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the files are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take a while to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
!ESPGUIFigure23.jpg|align=centre!
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
!ESPGUIFigure24.jpg|align=centre!
A window will open showing you the progress of the log file parsing.
!ESPGUIFigure25.jpg|align=centre!
Once the log interpretation is complete, you should see many more things in the calendar view.  In the figure below you will notice several new things.  The exclamation points in the middle of the mission bar on the calendar indicate an error during the run of the ESP and the calendar icons with green arrows at the bottom of the mission bar indicate protocols that were found in the log file.
!ESPGUIFigure26.jpg|align=centre!
At this point, we can begin to explore some information about the currently deployed ESP.  If you select the "Actual" tab in the lower left pane, you will see the list of protocols that were interpreted from the log file.  You see the name of the protocol, the start date and time, the target/actual volumes of the associated water sample and the difference between the target and actual (if there is one).
!ESPGUIFigure27.jpg|align=centre!


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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab'. NOTE: The color selector was used in an older version to display on the calendar but is no longer used and will be removed in the future, you can ignore the color chooser.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse over the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For this reason, we don't allow spaces in mission names.  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/15/2011 00:00:00 |
| End Date | The date at which the mission will end | 8/31/2011 00:00:00 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | ftp.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://ftp.mbari.org/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_ which means the host is _ftp.mbari.org_ and the FTP Root is _/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|align=centre!
# What you now see is a small calendar icon in the upper portion of the colored mission bar on the calendar.  It is place at the top of the mission bar to indicate that it is a planned protocol, not one that was extracted from the log file (which you will see later).  Also, the small pencil on the icon means that it is a planned protocol, not an actual one.  The small letter at the front of the icon is used to help distinguish the which protocol this is.  It is simply the first letter of the name that you gave the protocol.  You will alos notice the list of "Planned" protocols in the lower left pane shows the list of protocols you have planned so far.  I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the Protocol, Event and Data Window.  As mentioned above, the first tab "Planned" shows you the protocols that have been planned for this mission (what you created earlier). You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Images", "Errors" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates (which we will do shortly).  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the files are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take a while to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
!ESPGUIFigure23.jpg|align=centre!
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
!ESPGUIFigure24.jpg|align=centre!
A window will open showing you the progress of the log file parsing.
!ESPGUIFigure25.jpg|align=centre!
Once the log interpretation is complete, you should see many more things in the calendar view.  In the figure below you will notice several new things.  The exclamation points in the middle of the mission bar on the calendar indicate an error during the run of the ESP and the calendar icons with green arrows at the bottom of the mission bar indicate protocols that were found in the log file.
!ESPGUIFigure26.jpg|align=centre!

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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab'. NOTE: The color selector was used in an older version to display on the calendar but is no longer used and will be removed in the future, you can ignore the color chooser.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse over the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For this reason, we don't allow spaces in mission names.  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/15/2011 00:00:00 |
| End Date | The date at which the mission will end | 8/31/2011 00:00:00 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | ftp.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://ftp.mbari.org/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_ which means the host is _ftp.mbari.org_ and the FTP Root is _/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|align=centre!
# What you now see is a small calendar icon in the upper portion of the colored mission bar on the calendar.  It is place at the top of the mission bar to indicate that it is a planned protocol, not one that was extracted from the log file (which you will see later).  Also, the small pencil on the icon means that it is a planned protocol, not an actual one.  The small letter at the front of the icon is used to help distinguish the which protocol this is.  It is simply the first letter of the name that you gave the protocol.  You will alos notice the list of "Planned" protocols in the lower left pane shows the list of protocols you have planned so far.  I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the Protocol, Event and Data Window.  As mentioned above, the first tab "Planned" shows you the protocols that have been planned for this mission (what you created earlier). You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Images", "Errors" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates (which we will do shortly).  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the files are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take a while to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
!ESPGUIFigure23.jpg|align=centre!
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
!ESPGUIFigure24.jpg|align=centre!
A window will open showing you the progress of the log file parsing.
Figure 25
Log file during parsing
Figure 26
Log file parsing complete.
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab'. NOTE: The color selector was used in an older version to display on the calendar but is no longer used and will be removed in the future, you can ignore the color chooser.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse over the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For this reason, we don't allow spaces in mission names.  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/15/2011 00:00:00 |
| End Date | The date at which the mission will end | 8/31/2011 00:00:00 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | ftp.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://ftp.mbari.org/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_ which means the host is _ftp.mbari.org_ and the FTP Root is _/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|align=centre!
# What you now see is a small calendar icon in the upper portion of the colored mission bar on the calendar.  It is place at the top of the mission bar to indicate that it is a planned protocol, not one that was extracted from the log file (which you will see later).  Also, the small pencil on the icon means that it is a planned protocol, not an actual one.  The small letter at the front of the icon is used to help distinguish the which protocol this is.  It is simply the first letter of the name that you gave the protocol.  You will alos notice the list of "Planned" protocols in the lower left pane shows the list of protocols you have planned so far.  I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the Protocol, Event and Data Window.  As mentioned above, the first tab "Planned" shows you the protocols that have been planned for this mission (what you created earlier). You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Images", "Errors" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates (which we will do shortly).  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the files are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take a while to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
!ESPGUIFigure23.jpg|align=centre!
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
!ESPGUIFigure24.jpg|align=centre!
A window will open showing you the progress of the log file parsing.
!ESPGUIFigure25.jpg|align=centre!
Once the log interpretation is complete, you should see many more things in the calendar view.  In the figure below you will notice several new things.  The exclamation points in the middle of the mission bar on the calendar indicate an error during the run of the ESP and the calendar icons with green arrows at the bottom of the mission bar indicate protocols that were found in the log file.
!ESPGUIFigure26.jpg|align=centre!
At this point, we can begin to explore some information about the currently deployed ESP.  If you select the "Actual" tab in the lower left pane, you will see the list of protocols that were interpreted from the log file.  You see the name of the protocol, the start date and time, the target/actual volumes of the associated water sample and the difference between the target and actual (if there is one).
!ESPGUIFigure27.jpg|align=centre!
If you click on the protocol either in the calendar view or in the "Actual" table, you will see more details about the protocol in both the Protocol Graph Window and in the Context Sensitive Details Window.  In the following figure, I selected the first pcr protocol.
!ESPGUIFigure28.jpg|align=centre!
In the Protocol Graph Window you can see some details about the various related artifacts.  In this example, since this if from the Deep ESP, you can see that the water sample associated with the PCR itself was extracted from a DWSM sample.  You can also see the associated images that were taken of the analyzed sample associated with the PCR.  The WCR that is show gives you the information that there was indeed an archive performed in association with this PCR. In the context sensitive details window on the lower right side of the screen you can see the entry in the log file that the PCR protocol was extracted from.  If you select one of the images in the graph or switch to the "Images" tab, you will get more information about the image you have selected.
!ESPGUIFigure29.jpg|align=centre!
The image tab shows a table with some information about the selected image such as the date and time it was taken and the exposure that was used.  In the context sensitive details panel, you can see the image itself and if you select the "Metadata" tab you will see the information extracted from the TIFF image itself.  The "Log Entry" tab shows the location in the log file that this entry was extracted from.  Next if you select an Error exclamation point in the calendar view, or switch to the "Error" tab, you will get more information about the errors that were discovered in the log file.
!ESPGUIFigure30.jpg|align=centre!
In this example, you can see the error is the abort of the mission and when that error occurred.  In the context details window, you can see the log entry with a window of lines on both sides of the entry so you can see the context in which the error occurred. If you select the "Ancillary" tab, you can get information about the ancillary data that was extracted from the log file.  This is the data the is logged by sensors in the ESP itself in addition to other contextual sensors that are attached to the ESP and are logging their data through the ESP. In the example shown below, there is data available from the ESP Can itself as well as from an associated CTD and an ISUS.  If you select an appropriate time window (for this example, I chose Jul 17 through July 20, then choose the variables you are interested in and click "Refresh", you will see a plot of the various data in the context sensitive details window.
!ESPGUIFigure31.jpg|align=centre!
If you right-click on the plot itself, you will be presented with some options to save, print or zoom/pan the ancillary data plots.  If you want to save the data that you have plotted, in the left window, click on the "Save Selected" button and it will present you with a file dialog so you can save a comma separated list of data points to your disk somewhere for further analysis. Note that in the resulting CSV file, the dates and times of the different data do not align and so where there is not data "N/A"s are inserted as excel understands those as no data.
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab'. NOTE: The color selector was used in an older version to display on the calendar but is no longer used and will be removed in the future, you can ignore the color chooser.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse over the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For this reason, we don't allow spaces in mission names.  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/15/2011 00:00:00 |
| End Date | The date at which the mission will end | 8/31/2011 00:00:00 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | ftp.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://ftp.mbari.org/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_ which means the host is _ftp.mbari.org_ and the FTP Root is _/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|align=centre!
# What you now see is a small calendar icon in the upper portion of the colored mission bar on the calendar.  It is place at the top of the mission bar to indicate that it is a planned protocol, not one that was extracted from the log file (which you will see later).  Also, the small pencil on the icon means that it is a planned protocol, not an actual one.  The small letter at the front of the icon is used to help distinguish the which protocol this is.  It is simply the first letter of the name that you gave the protocol.  You will alos notice the list of "Planned" protocols in the lower left pane shows the list of protocols you have planned so far.  I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the Protocol, Event and Data Window.  As mentioned above, the first tab "Planned" shows you the protocols that have been planned for this mission (what you created earlier). You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Images", "Errors" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates (which we will do shortly).  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the files are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take a while to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
!ESPGUIFigure23.jpg|align=centre!
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
!ESPGUIFigure24.jpg|align=centre!
A window will open showing you the progress of the log file parsing.
!ESPGUIFigure25.jpg|align=centre!
Once the log interpretation is complete, you should see many more things in the calendar view.  In the figure below you will notice several new things.  The exclamation points in the middle of the mission bar on the calendar indicate an error during the run of the ESP and the calendar icons with green arrows at the bottom of the mission bar indicate protocols that were found in the log file.
!ESPGUIFigure26.jpg|align=centre!
At this point, we can begin to explore some information about the currently deployed ESP.  If you select the "Actual" tab in the lower left pane, you will see the list of protocols that were interpreted from the log file.  You see the name of the protocol, the start date and time, the target/actual volumes of the associated water sample and the difference between the target and actual (if there is one).
!ESPGUIFigure27.jpg|align=centre!
If you click on the protocol either in the calendar view or in the "Actual" table, you will see more details about the protocol in both the Protocol Graph Window and in the Context Sensitive Details Window.  In the following figure, I selected the first pcr protocol.
!ESPGUIFigure28.jpg|align=centre!
In the Protocol Graph Window you can see some details about the various related artifacts.  In this example, since this if from the Deep ESP, you can see that the water sample associated with the PCR itself was extracted from a DWSM sample.  You can also see the associated images that were taken of the analyzed sample associated with the PCR.  The WCR that is show gives you the information that there was indeed an archive performed in association with this PCR. In the context sensitive details window on the lower right side of the screen you can see the entry in the log file that the PCR protocol was extracted from.  If you select one of the images in the graph or switch to the "Images" tab, you will get more information about the image you have selected.
!ESPGUIFigure29.jpg|align=centre!
The image tab shows a table with some information about the selected image such as the date and time it was taken and the exposure that was used.  In the context sensitive details panel, you can see the image itself and if you select the "Metadata" tab you will see the information extracted from the TIFF image itself.  The "Log Entry" tab shows the location in the log file that this entry was extracted from.  Next if you select an Error exclamation point in the calendar view, or switch to the "Error" tab, you will get more information about the errors that were discovered in the log file.
!ESPGUIFigure30.jpg|align=centre!
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab'. NOTE: The color selector was used in an older version to display on the calendar but is no longer used and will be removed in the future, you can ignore the color chooser.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse over the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For this reason, we don't allow spaces in mission names.  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/15/2011 00:00:00 |
| End Date | The date at which the mission will end | 8/31/2011 00:00:00 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | ftp.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://ftp.mbari.org/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_ which means the host is _ftp.mbari.org_ and the FTP Root is _/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|align=centre!
# What you now see is a small calendar icon in the upper portion of the colored mission bar on the calendar.  It is place at the top of the mission bar to indicate that it is a planned protocol, not one that was extracted from the log file (which you will see later).  Also, the small pencil on the icon means that it is a planned protocol, not an actual one.  The small letter at the front of the icon is used to help distinguish the which protocol this is.  It is simply the first letter of the name that you gave the protocol.  You will alos notice the list of "Planned" protocols in the lower left pane shows the list of protocols you have planned so far.  I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the Protocol, Event and Data Window.  As mentioned above, the first tab "Planned" shows you the protocols that have been planned for this mission (what you created earlier). You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Images", "Errors" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates (which we will do shortly).  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the files are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take a while to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
!ESPGUIFigure23.jpg|align=centre!
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
!ESPGUIFigure24.jpg|align=centre!
A window will open showing you the progress of the log file parsing.
!ESPGUIFigure25.jpg|align=centre!
Once the log interpretation is complete, you should see many more things in the calendar view.  In the figure below you will notice several new things.  The exclamation points in the middle of the mission bar on the calendar indicate an error during the run of the ESP and the calendar icons with green arrows at the bottom of the mission bar indicate protocols that were found in the log file.
!ESPGUIFigure26.jpg|align=centre!
At this point, we can begin to explore some information about the currently deployed ESP.  If you select the "Actual" tab in the lower left pane, you will see the list of protocols that were interpreted from the log file.  You see the name of the protocol, the start date and time, the target/actual volumes of the associated water sample and the difference between the target and actual (if there is one).
!ESPGUIFigure27.jpg|align=centre!
If you click on the protocol either in the calendar view or in the "Actual" table, you will see more details about the protocol in both the Protocol Graph Window and in the Context Sensitive Details Window.  In the following figure, I selected the first pcr protocol.
!ESPGUIFigure28.jpg|align=centre!
In the Protocol Graph Window you can see some details about the various related artifacts.  In this example, since this if from the Deep ESP, you can see that the water sample associated with the PCR itself was extracted from a DWSM sample.  You can also see the associated images that were taken of the analyzed sample associated with the PCR.  The WCR that is show gives you the information that there was indeed an archive performed in association with this PCR. In the context sensitive details window on the lower right side of the screen you can see the entry in the log file that the PCR protocol was extracted from.  If you select one of the images in the graph or switch to the "Images" tab, you will get more information about the image you have selected.
!ESPGUIFigure29.jpg|align=centre!


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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|align=centre!

There are five areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "Protocol Graph Window" (middle left)
# "Protocol, Event, and Data Window" (lower left corner).
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab'. NOTE: The color selector was used in an older version to display on the calendar but is no longer used and will be removed in the future, you can ignore the color chooser.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse over the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For this reason, we don't allow spaces in mission names.  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/15/2011 00:00:00 |
| End Date | The date at which the mission will end | 8/31/2011 00:00:00 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | ftp.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://ftp.mbari.org/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_ which means the host is _ftp.mbari.org_ and the FTP Root is _/pub/kgomes/ESP/test/data/Gordon/JuanDeFuca_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|align=centre!
# What you now see is a small calendar icon in the upper portion of the colored mission bar on the calendar.  It is place at the top of the mission bar to indicate that it is a planned protocol, not one that was extracted from the log file (which you will see later).  Also, the small pencil on the icon means that it is a planned protocol, not an actual one.  The small letter at the front of the icon is used to help distinguish the which protocol this is.  It is simply the first letter of the name that you gave the protocol.  You will alos notice the list of "Planned" protocols in the lower left pane shows the list of protocols you have planned so far.  I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the Protocol, Event and Data Window.  As mentioned above, the first tab "Planned" shows you the protocols that have been planned for this mission (what you created earlier). You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Images", "Errors" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates (which we will do shortly).  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
The above figure shows some the control panel for the file synchronization with the FTP server.  The first button will simply open the directory on your local disk where the files are being stored so you can find them easily in your file manager.  The second button simply examines the remote and local file directories and refreshes the view of their status.  Assuming the light is green (and not red which would indicate that there is something incorrect with the FTP configuration in the mission and the GUI cannot connect to the FTP server), the last button will pull down the most recent version of the remote files on the FTP server and synchronize your local files to those on the remote FTP server.  Depending on your connection and the size of the files, this can sometimes take a while to perform.  Once this is done, all the files should show green to indicate they are synchronized with the FTP server.
!ESPGUIFigure23.jpg|align=centre!
After the sync, you should see copies of the files on your local hard drive.  Now with the files synchronized locally, you can tell the GUI to go ahead and parse the log file for information about protocols, samples, images, ancillary data, etc.  This can be done by right-clicking on either the mission in the Instrument Window or in the Calendar Window and selecting *Interpret Log*.
!ESPGUIFigure24.jpg|align=centre!
A window will open showing you the progress of the log file parsing.
!ESPGUIFigure25.jpg|align=centre!
Once the log interpretation is complete, you should see many more things in the calendar view.  In the figure below you will notice several new things.  The exclamation points in the middle of the mission bar on the calendar indicate an error during the run of the ESP and the calendar icons with green arrows at the bottom of the mission bar indicate protocols that were found in the log file.
!ESPGUIFigure26.jpg|align=centre!
At this point, we can begin to explore some information about the currently deployed ESP.  If you select the "Actual" tab in the lower left pane, you will see the list of protocols that were interpreted from the log file.  You see the name of the protocol, the start date and time, the target/actual volumes of the associated water sample and the difference between the target and actual (if there is one).
!ESPGUIFigure27.jpg|align=centre!
If you click on the protocol either in the calendar view or in the "Actual" table, you will see more details about the protocol in both the Protocol Graph Window and in the Context Sensitive Details Window.  In the following figure, I selected the first pcr protocol.
!ESPGUIFigure28.jpg|align=centre!


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<property name="body"><![CDATA[h2. IMEI number for the Melo tracker:


h1. *300034012090780*

User's Manuals
# [Quick Start Guide v1.2|^Xeos_Melo_manual-1.pdf|quick start]
# [User Manual v1.5|^Xeos_Melo_manual-2.pdf|Full Manual]
# [Watch Circle Console User Manual v2.1|^Xeos_Melo_manual-3.pdf|watch circle]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}

h4. Administrative Items

{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[# [4K Sphere]\\

h2. IEMI number for Sable 5000:


h1. 300034012099780

# [Sable 5000 Iridium Beacon Manual v. 2.0|^Xeos_Sable_manual.pdf|v2.0]
# [Sable 5000 Iridium Beacon Manual v. 2.1|^Xeos_Sable_Manual_2.1.pdf|v2.1]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}

h4. Administrative Items

{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}

h4. Administrative Items

{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[# [Lessons Learned from CMORE Hawaii cruise (Sep, 2011)]]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
\\
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage taken by Rob Vincent:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]

Map of locations:&nbsp; [http://maps.google.com/maps/ms?ie=UTF&msa=0&msid=213220825771739778963.0004a40bdd601babc291d]

May 23.&nbsp; Attempted recovery of ESP.&nbsp; Message from Roman:

{color:#996600}&nbsp;&nbsp;&nbsp; We went out to the site where espbruce was moored and attempted to find it.&nbsp; The weather was very poor and water was very turbid.&nbsp; Using the ships depth finder we found a promising target.&nbsp; In difficult conditions the divers performed a search but espbruce was not found.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; We recovered the mooring.&nbsp; It looks like the cable was pulled straight out of the cone.&nbsp; The top mast is bent but I cannot say if this was caused by a rough landing on the beach or boat impact.&nbsp; There are no dents or gouges on the mooring.&nbsp; The radio box is dry and antenna looks ok.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; Thursday the RV Gulf Challenger may be able to survey the area with a side scanning sonar.&nbsp; This will be a much better way to search for espbruce.&nbsp;{color}

Message from Roman May 26:

{color:#996600}&nbsp;&nbsp;&nbsp; ESPbruce was located at&nbsp; 43° 02.0740 N&nbsp;&nbsp; 70° 36.8447 W at ~ 10m depth.&nbsp; This position is about 19 yards from the waypoint.&nbsp; So looks like it wasn't dragged and has maintained seal integrity.&nbsp; We will attempt to recover it this weekend if we can get the RV Tioga.&nbsp; If not will recover with the RV Connecticut on june 7th weather permitting.{color}
&nbsp;

Dates for a recovery kept moving as weather and scheduling problems arose.&nbsp; Finally, Roman reported on June 15:
{quote}
{quote}
{color:#996600}ESPbruce was recovered today with no visible external damage. The EM cable strain relief is still on the cable.&nbsp; The recovery operation used two ships the RV Gulf Challenger and it's sister the RV Tioga.&nbsp; The Challenger supported the the side scan survey and the Tioga supported the divers and lifting of the core package and its anchor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;The side scan sonar operator advised me at the beginning of the day that he believed the esp package would be found on the bottom.&nbsp; He based this opinion on the data secured by his colleague almost two weeks ago.&nbsp; From his read of that run, he believed that the instrument was 15m off the bottom at that time.&nbsp; Depth at this site is 49m.&nbsp; He felt that the instrument was slowly sinking and that by today it was surly be on the sea floor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Todays side scan survey took approximately 90 minutes.&nbsp; They had acquired a strong signature on the core and calculated that it was at a depth of 65 feet (~20m). The package&nbsp; was still located within 10m of the original deployment site.&nbsp; They dropped a marker line with a float as close to the calculated position as possible.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;At this point divers equipped with twin 80 cu ft Nitrox cylinders and electric scooters dived on the marker.&nbsp; They had 70 minutes of search time.&nbsp; After 42 minutes an orange sausage float attached to a spectra lift line appeared.&nbsp; Then 10 minutes later a second lift bag attached to the EM cable appeared.&nbsp; The divers surfaced after a total bottom time of 62 minutes.&nbsp; Eight minutes to spare.&nbsp; We recovered the divers.&nbsp; They reported that the depth of top of the can was at 26 feet (~8m) right where it was supposed to be.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Recovery went smoothly using a single winch equipped with a capstan attachment.&nbsp; By alternately shifting the load from drum (used to lift anchor) and capstan (used to lift instrument we recovered the package and the anchor safely.{color}
{quote}
\\
\\  {color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford.

{color:#cc3300}July 6{color} \-\- Ship by truck D-ESP and supplies for JdF cruise.&nbsp; To Newport, OR.

{color:#cc3300}July 13{color} \-\- Sail for Axial and JdF (1 day late due to weather getting up to Newport)

{color:#cc0000}July 20{color} \-\- recall D-ESP.&nbsp; Recover all instruments.&nbsp; Two more days for Dave Clague.&nbsp; Ship returns July 23.
\\

Aug 17 \-\- Matson picks up loaded ESP van.&nbsp; Genset on truck putting out >530V so our reefer unit will not start.&nbsp; Decide to send due to late hour and ship leaving tomorrow.&nbsp; Van wt. w/ all ESP-Drifter gear: 15,000 lbs.

Sep 6 \-\- Drifting ESP deployed from Kilo Moana N of Station Aloha.&nbsp; Running Bruce w/ MFB ?.

Sep 17 \-\- Drifting ESP recovered.&nbsp; Gear shipped Oct 7 (via DHX and Matson), arrived at MBARI Oct 12.. ]]></property>
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<property name="body"><![CDATA[# [Lessons Learned from CMORE Hawaii cruise (Sept 2011)|^Lessons Learned.docx|Lessons Learned]]]></property>
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<property name="body"><![CDATA[h2.  Lessons Learned meeting after Drifter Cruise 
*

# [Lessons Learned from CMORE Hawaii cruise (Sept 2011)|^Lessons Learned.docx|Lessons Learned]]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision
# [25Jun2009]
# 02Jul2009 - no meeting; 4th of July break
# [09Jul2009]
# [16Jul2009]
# [23Jul2009]
# 30Jul2009 - Scott ran mtg; proposal preparation
# [06Aug2009]
# 13Aug2009 - cancelled; proposal/grant preparations
# [20Aug2009]
# 27Aug2009 - Jim Vacation; Scott in charge
# 03Sep2009 - Jim Vacation; Scott in charge
# [10Sep2009]
# [01Oct2009]
# [08Oct2009]
# [15Oct2009]
# [22Oct2009]
# 29Oct2009 - Jim LLNL;Engineering & Chris S. set-up schedule for next MARS
# [05Nov2009] \-meeting of all ESP team on 03Nov]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [The MFB User's Manual]
# [MFB 2007-08 Timeline |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB command help sheet|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1_7%2010_03_2008.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/Fluidics_worksheet_04Dec08.pdf]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

|| Event || Example || Rule Used || Information Parsed ||
| Mission Start | {noformat}."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"{noformat} |{noformat}^GoodNews\\.\\S+\\s+\\\"Starting\\s+w/pucks\\s+in\\s+tube\\s+(\\d+).*Subject=>\\\"(\\S+)\\s+begun\\\".*{noformat} | # Starting tube
# Mission name |
| Ancillary Data | {noformat}#\Can@13:19:34, 48.2V, 17.3C, 44% humidity, 14.5psia, 14.84V, 0.42A, 0.413A avg, 6.21W
CTD@13:24:25, 3.3694C, 999.623 decibars, 3.1914 S/m, 104.61%, -0.180 1/m, 0.33 ml/l, 3.0760C
ISUS@13:24:45, 24.460 uM/L no^3, -1.000 uM/L hs, 22.7800psu{noformat} | # First it removes all newlines from the log entry and then checks to see if the entry may have ancillary data by using the pattern {noformat}^Can@.*{noformat}
# If it matches, then it takes the original log entry, splits it by newlines (I replace '\' with newlines earlier in the process) and then pattern match each line with {noformat}^(\\S+)@(\\d\\d):(\\d\\d):(\\d\\d),(.*)${noformat} to search for time, source and the payload of the message. | # Source
# Time
# Payload | 
| Process Run Start with Archive | {noformat}#pcr sampling at most 1000ml, wcr at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml, wcr at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume
# Archive Target Volume | 
| Process Run Start without Archive  | {noformat}#bac wcr sampling at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

|| Event || Example || Rule Used || Information Parsed ||
| Mission Start | {noformat}."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"{noformat} |{noformat}^GoodNews\\.\\S+\\s+\\\"Starting\\s+w/pucks\\s+in\\s+tube\\s+(\\d+).*Subject=>\\\"(\\S+)\\s+begun\\\".*{noformat} | # Starting tube
# Mission name |
| Ancillary Data | {noformat}#\Can@13:19:34, 48.2V, 17.3C, 44% humidity, 14.5psia, 14.84V, 0.42A, 0.413A avg, 6.21W
CTD@13:24:25, 3.3694C, 999.623 decibars, 3.1914 S/m, 104.61%, -0.180 1/m, 0.33 ml/l, 3.0760C
ISUS@13:24:45, 24.460 uM/L no^3, -1.000 uM/L hs, 22.7800psu{noformat} | # First it removes all newlines from the log entry and then checks to see if the entry may have ancillary data by using the pattern {noformat}^Can@.*{noformat}
# If it matches, then it takes the original log entry, splits it by newlines (I replace '\' with newlines earlier in the process) and then pattern match each line with {noformat}^(\\S+)@(\\d\\d):(\\d\\d):(\\d\\d),(.*)${noformat} to search for time, source and the payload of the message. | # Source
# Time
# Payload | 
| Process Run Start with Archive | {noformat}#pcr sampling at most 1000ml, wcr at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml, wcr at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume
# Archive Target Volume | 
| Process Run Start without Archive  | {noformat}#bac wcr sampling at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume | 
| Start Sample | {noformat}{noformat} | {noformat}^Sampling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| Stop Sample | {noformat}{noformat} | {noformat}^Sampled\\s+(\\d+\\.*\\d*)ml.*${noformat} | Actual Volume | 
| DWSM Start Sample | {noformat}{noformat} | {noformat}^(Res|S)ample Bag inhaling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| DWSM Stop Sample | {noformat}{noformat} | {noformat}^Waiting up to (\\d+)s for (Res|S)ample Bag to stabilize.*${noformat} | Nothing | 
| Image Capture | {noformat}{noformat} | {noformat}^.*Exposing\\s+(\\d+)x(\\d+)\\s+pixel\\s+(\\d+)-bit\\s+image\\s+for\\s+(\\d+\\.*\\d*)\\s+seconds(.*.tif).*${noformat} | # X pixels
# Y pixels
# number of bits
# exposure
# file name | 
| Image Stats | {noformat}{noformat} | {noformat}^(.*)\\/([a-zA-Z0-9]+)(\\d{2})([a-zA-Z]{3})(\\d{2})(\\d{2})h(\\d+)ml(\\d+)*s*\\.tif${noformat} | | 

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
\\
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage taken by Rob Vincent:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]

Map of locations:&nbsp; [http://maps.google.com/maps/ms?ie=UTF&msa=0&msid=213220825771739778963.0004a40bdd601babc291d]

May 23.&nbsp; Attempted recovery of ESP.&nbsp; Message from Roman:

{color:#996600}&nbsp;&nbsp;&nbsp; We went out to the site where espbruce was moored and attempted to find it.&nbsp; The weather was very poor and water was very turbid.&nbsp; Using the ships depth finder we found a promising target.&nbsp; In difficult conditions the divers performed a search but espbruce was not found.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; We recovered the mooring.&nbsp; It looks like the cable was pulled straight out of the cone.&nbsp; The top mast is bent but I cannot say if this was caused by a rough landing on the beach or boat impact.&nbsp; There are no dents or gouges on the mooring.&nbsp; The radio box is dry and antenna looks ok.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; Thursday the RV Gulf Challenger may be able to survey the area with a side scanning sonar.&nbsp; This will be a much better way to search for espbruce.&nbsp;{color}

Message from Roman May 26:

{color:#996600}&nbsp;&nbsp;&nbsp; ESPbruce was located at&nbsp; 43° 02.0740 N&nbsp;&nbsp; 70° 36.8447 W at ~ 10m depth.&nbsp; This position is about 19 yards from the waypoint.&nbsp; So looks like it wasn't dragged and has maintained seal integrity.&nbsp; We will attempt to recover it this weekend if we can get the RV Tioga.&nbsp; If not will recover with the RV Connecticut on june 7th weather permitting.{color}
&nbsp;

Dates for a recovery kept moving as weather and scheduling problems arose.&nbsp; Finally, Roman reported on June 15:
{quote}
{quote}
{color:#996600}ESPbruce was recovered today with no visible external damage. The EM cable strain relief is still on the cable.&nbsp; The recovery operation used two ships the RV Gulf Challenger and it's sister the RV Tioga.&nbsp; The Challenger supported the the side scan survey and the Tioga supported the divers and lifting of the core package and its anchor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;The side scan sonar operator advised me at the beginning of the day that he believed the esp package would be found on the bottom.&nbsp; He based this opinion on the data secured by his colleague almost two weeks ago.&nbsp; From his read of that run, he believed that the instrument was 15m off the bottom at that time.&nbsp; Depth at this site is 49m.&nbsp; He felt that the instrument was slowly sinking and that by today it was surly be on the sea floor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Todays side scan survey took approximately 90 minutes.&nbsp; They had acquired a strong signature on the core and calculated that it was at a depth of 65 feet (~20m). The package&nbsp; was still located within 10m of the original deployment site.&nbsp; They dropped a marker line with a float as close to the calculated position as possible.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;At this point divers equipped with twin 80 cu ft Nitrox cylinders and electric scooters dived on the marker.&nbsp; They had 70 minutes of search time.&nbsp; After 42 minutes an orange sausage float attached to a spectra lift line appeared.&nbsp; Then 10 minutes later a second lift bag attached to the EM cable appeared.&nbsp; The divers surfaced after a total bottom time of 62 minutes.&nbsp; Eight minutes to spare.&nbsp; We recovered the divers.&nbsp; They reported that the depth of top of the can was at 26 feet (~8m) right where it was supposed to be.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Recovery went smoothly using a single winch equipped with a capstan attachment.&nbsp; By alternately shifting the load from drum (used to lift anchor) and capstan (used to lift instrument we recovered the package and the anchor safely.{color}
{quote}
\\
\\  {color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford.

{color:#cc3300}July 6{color} \-\- Ship by truck D-ESP and supplies for JdF cruise.&nbsp; To Newport, OR.

{color:#cc3300}July 13{color} \-\- Sail for Axial and JdF (1 day late due to weather getting up to Newport)

{color:#cc0000}July 20{color} \-\- recall D-ESP.&nbsp; Recover all instruments.&nbsp; Two more days for Dave Clague.&nbsp; Ship returns July 23.
\\

Aug 17 \-\- Matson picks up loaded ESP van.&nbsp; Genset on truck putting out >530V so our reefer unit will not start.&nbsp; Decide to send due to late hour and ship leaving tomorrow.&nbsp; Van wt. w/ all ESP-Drifter gear: 15,000 lbs.

Sep 6 \-\- Drifting ESP deployed from Kilo Moana N of Station Aloha.&nbsp; Running Bruce w/ MFB ?.

Sep 17 \-\- Drifting ESP recovered.&nbsp; Gear to be shipped home Oct 7, arriving Oct 11. ]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

|| Event || Example || Rule Used || Information Parsed ||
| Mission Start | {noformat}."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"{noformat} |{noformat}^GoodNews\\.\\S+\\s+\\\"Starting\\s+w/pucks\\s+in\\s+tube\\s+(\\d+).*Subject=>\\\"(\\S+)\\s+begun\\\".*{noformat} | # Starting tube
# Mission name |
| Ancillary Data | {noformat}#\Can@13:19:34, 48.2V, 17.3C, 44% humidity, 14.5psia, 14.84V, 0.42A, 0.413A avg, 6.21W
CTD@13:24:25, 3.3694C, 999.623 decibars, 3.1914 S/m, 104.61%, -0.180 1/m, 0.33 ml/l, 3.0760C
ISUS@13:24:45, 24.460 uM/L no^3, -1.000 uM/L hs, 22.7800psu{noformat} | # First it removes all newlines from the log entry and then checks to see if the entry may have ancillary data by using the pattern {noformat}^Can@.*{noformat}
# If it matches, then it takes the original log entry, splits it by newlines (I replace '\' with newlines earlier in the process) and then pattern match each line with {noformat}^(\\S+)@(\\d\\d):(\\d\\d):(\\d\\d),(.*)${noformat} to search for time, source and the payload of the message. | # Source
# Time
# Payload | 
| Process Run Start with Archive | {noformat}#pcr sampling at most 1000ml, wcr at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml, wcr at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume
# Archive Target Volume | 
| Process Run Start without Archive  | {noformat}#bac wcr sampling at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume | 
| Start Sample | {noformat}#t\Sampling 100.0ml{noformat} | {noformat}^Sampling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| Stop Sample | {noformat}#t\Sampled  100.0ml{noformat} | {noformat}^Sampled\\s+(\\d+\\.*\\d*)ml.*${noformat} | Actual Volume | 
| DWSM Start Sample | {noformat}#t\Sample Bag inhaling 5000.0ml{noformat} | {noformat}^Sample Bag inhaling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| DWSM Stop Sample | {noformat}#tWaiting up to 90s for Sample Bag to stabilize at 2279.4psia +/-25.0{noformat} | {noformat}^Waiting up to (\\d+)s for Sample Bag to stabilize.*${noformat} | Nothing | 
| Image Capture | {noformat}#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
\Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr11jul1500h2000ml40s.tif: TIFF Upload Complete{noformat} | Uses two patterns: 
# One
{noformat}^.*Exposing\\s+(\\d+)x(\\d+)\\s+pixel\\s+(\\d+)-bit\\s+image\\s+for\\s+(\\d+\\.*\\d*)\\s+seconds(.*.tif).*${noformat}
# Two 
{noformat}^(.*)\\/([a-zA-Z0-9]+)(\\d{2})([a-zA-Z]{3})(\\d{2})(\\d{2})h(\\d+)ml(\\d+)*s*\\.tif${noformat} | # One
## Image file name
# Two
## ProcessRun name
## Exposure Time | 
| Errors | {noformat}."Qmail"BadNews.suppressMail "Aborted by MAIN during Intake/Exhaust Pump move",:Subject=>"Thread::Aborted in readyDWSM"{noformat} | {noformat}BadNews.\\S+\\s+\"(.*)\",:Subject=>\"(.*)\"{noformat} | Error Message |

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

|| Event || Example || Rule Used || Information Parsed ||
| Mission Start | {noformat}."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"{noformat} |{noformat}^GoodNews\\.\\S+\\s+\\\"Starting\\s+w/pucks\\s+in\\s+tube\\s+(\\d+).*Subject=>\\\"(\\S+)\\s+begun\\\".*{noformat} | # Starting tube
# Mission name |
| Ancillary Data | {noformat}#\Can@13:19:34, 48.2V, 17.3C, 44% humidity, 14.5psia, 14.84V, 0.42A, 0.413A avg, 6.21W
CTD@13:24:25, 3.3694C, 999.623 decibars, 3.1914 S/m, 104.61%, -0.180 1/m, 0.33 ml/l, 3.0760C
ISUS@13:24:45, 24.460 uM/L no^3, -1.000 uM/L hs, 22.7800psu{noformat} | # First it removes all newlines from the log entry and then checks to see if the entry may have ancillary data by using the pattern {noformat}^Can@.*{noformat}
# If it matches, then it takes the original log entry, splits it by newlines (I replace '\' with newlines earlier in the process) and then pattern match each line with {noformat}^(\\S+)@(\\d\\d):(\\d\\d):(\\d\\d),(.*)${noformat} to search for time, source and the payload of the message. | # Source
# Time
# Payload | 
| Process Run Start with Archive | {noformat}#pcr sampling at most 1000ml, wcr at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml, wcr at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume
# Archive Target Volume | 
| Process Run Start without Archive  | {noformat}#bac wcr sampling at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume | 
| Start Sample | {noformat}#t\Sampling 100.0ml{noformat} | {noformat}^Sampling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| Stop Sample | {noformat}#t\Sampled  100.0ml{noformat} | {noformat}^Sampled\\s+(\\d+\\.*\\d*)ml.*${noformat} | Actual Volume | 
| DWSM Start Sample | {noformat}#t\Sample Bag inhaling 5000.0ml{noformat} | {noformat}^Sample Bag inhaling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| DWSM Stop Sample | {noformat}#tWaiting up to 90s for Sample Bag to stabilize at 2279.4psia +/-25.0{noformat} | {noformat}^Waiting up to (\\d+)s for Sample Bag to stabilize.*${noformat} | Nothing | 
| Image Capture | {noformat}#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\Exposing 696x520 pixel 16-bit image for 40 seconds\/var/log/esp/pcr11jul1500h2000ml40s.tif: TIFF Upload Complete\{noformat} | Uses two patterns: 
# One
{noformat}^.*Exposing\\s+(\\d+)x(\\d+)\\s+pixel\\s+(\\d+)-bit\\s+image\\s+for\\s+(\\d+\\.*\\d*)\\s+seconds(.*.tif).*${noformat}
# Two 
{noformat}^(.*)\\/([a-zA-Z0-9]+)(\\d{2})([a-zA-Z]{3})(\\d{2})(\\d{2})h(\\d+)ml(\\d+)*s*\\.tif${noformat} | # One
## Image file name
# Two
## ProcessRun name
## Exposure Time | 
| Errors | {noformat}."Qmail"BadNews.suppressMail "Aborted by MAIN during Intake/Exhaust Pump move",:Subject=>"Thread::Aborted in readyDWSM"{noformat} | {noformat}BadNews.\\S+\\s+\"(.*)\",:Subject=>\"(.*)\"{noformat} | Error Message |

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

|| Event || Example || Rule Used || Information Parsed ||
| Mission Start | {noformat}."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"{noformat} |{noformat}^GoodNews\\.\\S+\\s+\\\"Starting\\s+w/pucks\\s+in\\s+tube\\s+(\\d+).*Subject=>\\\"(\\S+)\\s+begun\\\".*{noformat} | # Starting tube
# Mission name |
| Ancillary Data | {noformat}#\Can@13:19:34, 48.2V, 17.3C, 44% humidity, 14.5psia, 14.84V, 0.42A, 0.413A avg, 6.21W
CTD@13:24:25, 3.3694C, 999.623 decibars, 3.1914 S/m, 104.61%, -0.180 1/m, 0.33 ml/l, 3.0760C
ISUS@13:24:45, 24.460 uM/L no^3, -1.000 uM/L hs, 22.7800psu{noformat} | # First it removes all newlines from the log entry and then checks to see if the entry may have ancillary data by using the pattern {noformat}^Can@.*{noformat}
# If it matches, then it takes the original log entry, splits it by newlines (I replace '\' with newlines earlier in the process) and then pattern match each line with {noformat}^(\\S+)@(\\d\\d):(\\d\\d):(\\d\\d),(.*)${noformat} to search for time, source and the payload of the message. | # Source
# Time
# Payload | 
| Process Run Start with Archive | {noformat}#pcr sampling at most 1000ml, wcr at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml, wcr at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume
# Archive Target Volume | 
| Process Run Start without Archive  | {noformat}#bac wcr sampling at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume | 
| Start Sample | {noformat}#t\Sampling 100.0ml{noformat} | {noformat}^Sampling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| Stop Sample | {noformat}#t\Sampled  100.0ml{noformat} | {noformat}^Sampled\\s+(\\d+\\.*\\d*)ml.*${noformat} | Actual Volume | 
| DWSM Start Sample | {noformat}#t\Sample Bag inhaling 5000.0ml{noformat} | {noformat}^Sample Bag inhaling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| DWSM Stop Sample | {noformat}#tWaiting up to 90s for Sample Bag to stabilize at 2279.4psia +/-25.0{noformat} | {noformat}^Waiting up to (\\d+)s for Sample Bag to stabilize.*${noformat} | Nothing | 
| Image Capture | {noformat}#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr11jul1500h2000ml40s.tif: TIFF Upload Complete\{noformat} | Uses two patterns: # One
{noformat}^.*Exposing\\s+(\\d+)x(\\d+)\\s+pixel\\s+(\\d+)-bit\\s+image\\s+for\\s+(\\d+\\.*\\d*)\\s+seconds(.*.tif).*${noformat}
# Two 
{noformat}^(.*)\\/([a-zA-Z0-9]+)(\\d{2})([a-zA-Z]{3})(\\d{2})(\\d{2})h(\\d+)ml(\\d+)*s*\\.tif${noformat} | # One
## Image file name
# Two
## ProcessRun name
## Exposure Time | 
| Errors | {noformat}."Qmail"BadNews.suppressMail "Aborted by MAIN during Intake/Exhaust Pump move",:Subject=>"Thread::Aborted in readyDWSM"{noformat} | {noformat}BadNews.\\S+\\s+\"(.*)\",:Subject=>\"(.*)\"{noformat} | Error Message |

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

|| Event || Example || Rule Used || Information Parsed ||
| Mission Start | {noformat}."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"{noformat} |{noformat}^GoodNews\\.\\S+\\s+\\\"Starting\\s+w/pucks\\s+in\\s+tube\\s+(\\d+).*Subject=>\\\"(\\S+)\\s+begun\\\".*{noformat} | # Starting tube
# Mission name |
| Ancillary Data | {noformat}#\Can@13:19:34, 48.2V, 17.3C, 44% humidity, 14.5psia, 14.84V, 0.42A, 0.413A avg, 6.21W
CTD@13:24:25, 3.3694C, 999.623 decibars, 3.1914 S/m, 104.61%, -0.180 1/m, 0.33 ml/l, 3.0760C
ISUS@13:24:45, 24.460 uM/L no^3, -1.000 uM/L hs, 22.7800psu{noformat} | # First it removes all newlines from the log entry and then checks to see if the entry may have ancillary data by using the pattern {noformat}^Can@.*{noformat}
# If it matches, then it takes the original log entry, splits it by newlines (I replace '\' with newlines earlier in the process) and then pattern match each line with {noformat}^(\\S+)@(\\d\\d):(\\d\\d):(\\d\\d),(.*)${noformat} to search for time, source and the payload of the message. | # Source
# Time
# Payload | 
| Process Run Start with Archive | {noformat}#pcr sampling at most 1000ml, wcr at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml, wcr at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume
# Archive Target Volume | 
| Process Run Start without Archive  | {noformat}#bac wcr sampling at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume | 
| Start Sample | {noformat}#t\Sampling 100.0ml{noformat} | {noformat}^Sampling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| Stop Sample | {noformat}#t\Sampled  100.0ml{noformat} | {noformat}^Sampled\\s+(\\d+\\.*\\d*)ml.*${noformat} | Actual Volume | 
| DWSM Start Sample | {noformat}#t\Sample Bag inhaling 5000.0ml{noformat} | {noformat}^Sample Bag inhaling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| DWSM Stop Sample | {noformat}#tWaiting up to 90s for Sample Bag to stabilize at 2279.4psia +/-25.0{noformat} | {noformat}^Waiting up to (\\d+)s for Sample Bag to stabilize.*${noformat} | Nothing | 
| Image Capture | {noformat}#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr11jul1500h2000ml40s.tif: TIFF Upload Complete\{noformat} | Uses two patterns: 
# One
{noformat}^.*Exposing\\s+(\\d+)x(\\d+)\\s+pixel\\s+(\\d+)-bit\\s+image\\s+for\\s+(\\d+\\.*\\d*)\\s+seconds(.*.tif).*${noformat}
# Two 
{noformat}^(.*)\\/([a-zA-Z0-9]+)(\\d{2})([a-zA-Z]{3})(\\d{2})(\\d{2})h(\\d+)ml(\\d+)*s*\\.tif${noformat} | # One
## Image file name
# Two
## ProcessRun name
## Exposure Time | 
| Errors | {noformat}."Qmail"BadNews.suppressMail "Aborted by MAIN during Intake/Exhaust Pump move",:Subject=>"Thread::Aborted in readyDWSM"{noformat} | {noformat}BadNews.\\S+\\s+\"(.*)\",:Subject=>\"(.*)\"{noformat} | Error Message |

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

|| Event || Example || Rule Used || Information Parsed ||
| Mission Start | {noformat}."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"{noformat} |{noformat}^GoodNews\\.\\S+\\s+\\\"Starting\\s+w/pucks\\s+in\\s+tube\\s+(\\d+).*Subject=>\\\"(\\S+)\\s+begun\\\".*{noformat} | # Starting tube
# Mission name |
| Ancillary Data | {noformat}#\Can@13:19:34, 48.2V, 17.3C, 44% humidity, 14.5psia, 14.84V, 0.42A, 0.413A avg, 6.21W
CTD@13:24:25, 3.3694C, 999.623 decibars, 3.1914 S/m, 104.61%, -0.180 1/m, 0.33 ml/l, 3.0760C
ISUS@13:24:45, 24.460 uM/L no^3, -1.000 uM/L hs, 22.7800psu{noformat} | # First it removes all newlines from the log entry and then checks to see if the entry may have ancillary data by using the pattern {noformat}^Can@.*{noformat}
# If it matches, then it takes the original log entry, splits it by newlines (I replace '\' with newlines earlier in the process) and then pattern match each line with {noformat}^(\\S+)@(\\d\\d):(\\d\\d):(\\d\\d),(.*)${noformat} to search for time, source and the payload of the message. | # Source
# Time
# Payload | 
| Process Run Start with Archive | {noformat}#pcr sampling at most 1000ml, wcr at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml, wcr at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume
# Archive Target Volume | 
| Process Run Start without Archive  | {noformat}#bac wcr sampling at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume | 
| Start Sample | {noformat}#t\Sampling 100.0ml{noformat} | {noformat}^Sampling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| Stop Sample | {noformat}#t\Sampled  100.0ml{noformat} | {noformat}^Sampled\\s+(\\d+\\.*\\d*)ml.*${noformat} | Actual Volume | 
| DWSM Start Sample | {noformat}#t\Sample Bag inhaling 5000.0ml{noformat} | {noformat}^Sample Bag inhaling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| DWSM Stop Sample | {noformat}#tWaiting up to 90s for Sample Bag to stabilize at 2279.4psia +/-25.0{noformat} | {noformat}^Waiting up to (\\d+)s for Sample Bag to stabilize.*${noformat} | Nothing | 
| Image Capture | {noformat}#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\{noformat}
{noformat}Exposing 696x520 pixel 16-bit image for 40 seconds\{noformat}
{noformat}/var/log/esp/pcr11jul1500h2000ml40s.tif: TIFF Upload Complete\{noformat} | Uses two patterns: # One
{noformat}^.*Exposing\\s+(\\d+)x(\\d+)\\s+pixel\\s+(\\d+)-bit\\s+image\\s+for\\s+(\\d+\\.*\\d*)\\s+seconds(.*.tif).*${noformat}
# Two 
{noformat}^(.*)\\/([a-zA-Z0-9]+)(\\d{2})([a-zA-Z]{3})(\\d{2})(\\d{2})h(\\d+)ml(\\d+)*s*\\.tif${noformat} | # One
## Image file name
# Two
## ProcessRun name
## Exposure Time | 
| Errors | {noformat}."Qmail"BadNews.suppressMail "Aborted by MAIN during Intake/Exhaust Pump move",:Subject=>"Thread::Aborted in readyDWSM"{noformat} | {noformat}BadNews.\\S+\\s+\"(.*)\",:Subject=>\"(.*)\"{noformat} | Error Message |

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

|| Event || Example || Rule Used || Information Parsed ||
| Mission Start | {noformat}."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"{noformat} |{noformat}^GoodNews\\.\\S+\\s+\\\"Starting\\s+w/pucks\\s+in\\s+tube\\s+(\\d+).*Subject=>\\\"(\\S+)\\s+begun\\\".*{noformat} | # Starting tube
# Mission name |
| Ancillary Data | {noformat}#\Can@13:19:34, 48.2V, 17.3C, 44% humidity, 14.5psia, 14.84V, 0.42A, 0.413A avg, 6.21W
CTD@13:24:25, 3.3694C, 999.623 decibars, 3.1914 S/m, 104.61%, -0.180 1/m, 0.33 ml/l, 3.0760C
ISUS@13:24:45, 24.460 uM/L no^3, -1.000 uM/L hs, 22.7800psu{noformat} | # First it removes all newlines from the log entry and then checks to see if the entry may have ancillary data by using the pattern {noformat}^Can@.*{noformat}
# If it matches, then it takes the original log entry, splits it by newlines (I replace '\' with newlines earlier in the process) and then pattern match each line with {noformat}^(\\S+)@(\\d\\d):(\\d\\d):(\\d\\d),(.*)${noformat} to search for time, source and the payload of the message. | # Source
# Time
# Payload | 
| Process Run Start with Archive | {noformat}#pcr sampling at most 1000ml, wcr at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml, wcr at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume
# Archive Target Volume | 
| Process Run Start without Archive  | {noformat}#bac wcr sampling at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume | 
| Start Sample | {noformat}#t\Sampling 100.0ml{noformat} | {noformat}^Sampling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| Stop Sample | {noformat}#t\Sampled  100.0ml{noformat} | {noformat}^Sampled\\s+(\\d+\\.*\\d*)ml.*${noformat} | Actual Volume | 
| DWSM Start Sample | {noformat}#t\Sample Bag inhaling 5000.0ml{noformat} | {noformat}^Sample Bag inhaling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| DWSM Stop Sample | {noformat}#tWaiting up to 90s for Sample Bag to stabilize at 2279.4psia +/-25.0{noformat} | {noformat}^Waiting up to (\\d+)s for Sample Bag to stabilize.*${noformat} | Nothing | 
| Image Capture | {noformat}#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr11jul1500h2000ml40s.tif: TIFF Upload Complete\{noformat} | Uses two patterns:
# One
{noformat}^.*Exposing\\s+(\\d+)x(\\d+)\\s+pixel\\s+(\\d+)-bit\\s+image\\s+for\\s+(\\d+\\.*\\d*)\\s+seconds(.*.tif).*${noformat}
# Two 
{noformat}^(.*)\\/([a-zA-Z0-9]+)(\\d{2})([a-zA-Z]{3})(\\d{2})(\\d{2})h(\\d+)ml(\\d+)*s*\\.tif${noformat} | # One
## Image file name
# Two
## ProcessRun name
## Exposure Time | 
| Errors | {noformat}."Qmail"BadNews.suppressMail "Aborted by MAIN during Intake/Exhaust Pump move",:Subject=>"Thread::Aborted in readyDWSM"{noformat} | {noformat}BadNews.\\S+\\s+\"(.*)\",:Subject=>\"(.*)\"{noformat} | Error Message |

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

|| Event || Example || Rule Used || Information Parsed ||
| Mission Start | {noformat}."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"{noformat} |{noformat}^GoodNews\\.\\S+\\s+\\\"Starting\\s+w/pucks\\s+in\\s+tube\\s+(\\d+).*Subject=>\\\"(\\S+)\\s+begun\\\".*{noformat} | # Starting tube
# Mission name |
| Ancillary Data | {noformat}#\Can@13:19:34, 48.2V, 17.3C, 44% humidity, 14.5psia, 14.84V, 0.42A, 0.413A avg, 6.21W
CTD@13:24:25, 3.3694C, 999.623 decibars, 3.1914 S/m, 104.61%, -0.180 1/m, 0.33 ml/l, 3.0760C
ISUS@13:24:45, 24.460 uM/L no^3, -1.000 uM/L hs, 22.7800psu{noformat} | # First it removes all newlines from the log entry and then checks to see if the entry may have ancillary data by using the pattern {noformat}^Can@.*{noformat}
# If it matches, then it takes the original log entry, splits it by newlines (I replace '\' with newlines earlier in the process) and then pattern match each line with {noformat}^(\\S+)@(\\d\\d):(\\d\\d):(\\d\\d),(.*)${noformat} to search for time, source and the payload of the message. | # Source
# Time
# Payload | 
| Process Run Start with Archive | {noformat}#pcr sampling at most 1000ml, wcr at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml, wcr at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume
# Archive Target Volume | 
| Process Run Start without Archive  | {noformat}#bac wcr sampling at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume | 
| Start Sample | {noformat}{noformat} | {noformat}^Sampling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| Stop Sample | {noformat}{noformat} | {noformat}^Sampled\\s+(\\d+\\.*\\d*)ml.*${noformat} | Actual Volume | 
| DWSM Start Sample | {noformat}{noformat} | {noformat}^(Res|S)ample Bag inhaling\\s+(\\d+\\.*\\d*)ml.*${noformat} | Target Volume | 
| DWSM Stop Sample | {noformat}{noformat} | {noformat}^Waiting up to (\\d+)s for (Res|S)ample Bag to stabilize.*${noformat} | Nothing | 
| Image Capture | {noformat}{noformat} | {noformat}^.*Exposing\\s+(\\d+)x(\\d+)\\s+pixel\\s+(\\d+)-bit\\s+image\\s+for\\s+(\\d+\\.*\\d*)\\s+seconds(.*.tif).*${noformat} | # X pixels
# Y pixels
# number of bits
# exposure
# file name | 
| Image Stats | {noformat}{noformat} | {noformat}^(.*)\\/([a-zA-Z0-9]+)(\\d{2})([a-zA-Z]{3})(\\d{2})(\\d{2})h(\\d+)ml(\\d+)*s*\\.tif${noformat} | | 
| Errors | {no format}{no format} | {no format}{no format} | |

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

]]></property>
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<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically (colors are same deployment)+

{color:#ff00ff}April 6--Bruce at M0 for surface deployment (Zephyr){color}

April 15--Mack in Sphere (dive #1) for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in Sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

{color:#ff00ff}April 29--Recover Bruce at M0 (Zephyr){color}

May 1--Mack in Sphere (dive #3) connected to DWSM; incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

{color:#0033cc}May 14--Deploy NEO w/PCR, surface deployment (Zephyr){color}

May 27--First Drifter dive; used weighted cable (Zephyr)

June 5-9 \-\- Western Flyer Trip.&nbsp; D-ESP, Drifter, and CTD casts. {color:#cc0000}{*}MOVIES{*}{color}:  D-ESP launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/DESP%20deployment%20(full%20quality).dv].  Drifter launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/Drifter.dv].

{color:#0033cc}June 11 \-\- Recover NEO.&nbsp; (Zephyr){color}\\

+FALL Network Deployment+

Proposed locations are here: [http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&msid=113879459163411006053.000471828af997bd7d89c&t=h&z=12]

{color:#ff6600}September 24 \-\- Deploy Moe w/PCR at M0.&nbsp; Deployed Mack at Santa Cruz{color}.&nbsp; {color:#66cc00}Deployed Bruce in the bight.&nbsp; (Zephyr)&nbsp; Lost communications with Bruce that day.{color}

{color:#66cc00}September 28 \-\- Recover (dead) Bruce.&nbsp; Comms box had water in it, but radio worked.&nbsp; EM cable had 2 broken wires. (Zephyr){color}

{color:#cc0000}September 30 \-\- Deploy D-ESP on MARS (Lobos).{color}&nbsp; Hand issue at first, but 'fixed' itself.&nbsp; Worked until Oct. 7 when wrong puck was loaded and water introduced into core, frying puck heater.&nbsp; We turned off and first recovery day (Oct 13) is weathered out.&nbsp; It still awaits recovery.

{color:#66cc00}October 14 \-\- Re-deploy Bruce (Zephyr).&nbsp; New comms box, re-terminated EM cable.&nbsp; Working well after deployment.{color}

October 20 \-\- Install pump system on pier at Santa Cruz Wharf. October 22 \-\- Neo installed on SC Wharf.

{color:#cc0000}October 30 \-\- Recover D-ESP off MARS (Lobos).{color}

{color:#ff6600}October 29 \-\- Recover both Moe from M0 and Mack from Santa Cruz (Zephyr).{color}

{color:#66cc00}November 2 \-\- Recover Bruce from the bight (Zephyr).&nbsp; This ends Fall Network Deployment.{color}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}

h4. Administrative Items

{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h2. Below are links to attached Word Documents

# [Spring 2010|^ESP G3 project overview.doc|first pass FR for G3]
# [Nov 11, 2010|^ESP G3 project requirements.doc|second pass FR for G3]
# [Sep 15, 2011|^Funct Req Sept 15 2011.docx|third pass FR for G3]]]></property>
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<property name="body"><![CDATA[# [https://oceana.mbari.org/confluence/users/insertlink-page-uploadfile.action#]]]></property>
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<property name="body"><![CDATA[# [v. 1.0.4]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB 2007-08 Timeline |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB command help sheet|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1_7%2010_03_2008.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/Fluidics_worksheet_04Dec08.pdf]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]]]></property>
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<property name="body"><![CDATA[# [G3 functional Requirements]]]></property>
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<property name="body"><![CDATA[# [G3 functional Requirements--Spring 2010|^ESP G3 project overview.doc|first pass FR for G3]]]></property>
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<property name="body"><![CDATA[This is a quick sequence of steps to get the user up and running with the ESP GUI application. When you first start up the ESP GUI application, it will look quite bland (we are working on that) :).

!ESPGUIFigure1.jpg|thumbnail,align=centre!

There are four main areas in the ESP GUI:
# "Instrument List Window" (upper left corner)
# "Calendar Window" (upper right corner)
# "ESP and Mission Tabs Window" (lower left corner)
# "Context Sensitive Details Window" (lower right corner).

!ESPGUIFigure2.jpg|thumbnail,align=centre!

You will get the idea behind these windows as we work through these examples.

h5. Configuration

Before getting started, it is best to take care of a couple of settings in the ESP GUI application.  If you go to the *ESP* menu and select *Preferences...*, you will see some settings that are common across all instruments and missions.
!ESPGUIFigure0_1.jpg|align=centre!
The *Local Storage: Directory* field indicates the local disk path where the application will store copies of the various mission files that the GUI works with.  It defaults to the user's home directory, but it can be changed.  The GUI application will append a directory with the ESP's name and another directory for the mission name to divide up the local storage of mission related files.  For example, in the above figure, the base local directory for data storage is _/Users/kgomes/esp_data_.  If I create ESP named _Gordon_ and create a mission for Gordon called _JuanDeFuca_, the files for that mission will be stored on the local disk in the directory:
{noformat}
/Users/kgomes/esp_data/Gordon/JuanDeFuca
{noformat}
In the *WebDAV Storage* section, these settings give the application the information it needs to store all the products and files for the various ESP's and their missions on a WebDAV server.  This function was created to assist end users by allowing them to send their files to a central WebDAV repository where technical support could review them and offer assistance.  Think of it as a way for the ESP to "call home".
# *Protocol*: This will either be "https" or "http", but should really be https.
# *Hostname*: This is the hostname of the WebDAV server where the files will be copied to.  In MBARI's case we use an Alfresco content management server.
# *Base URL*: This is the base URL where the files will be copied to.  In this example, there is a WebDAV directory structure that looks like:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP
{noformat}
which serves as the base for the file locations.  Using the example above, if we have the ESP Gordon running a mission called "JuanDeFuca", the directory structure that will be created for the files is:
{noformat}
https://alfresco.mbari.org/alfresco/webdav/Data/ESP/Gordon/JuanDeFuca
{noformat}
# *Username*: The login to the WebDAV server
# *Password/Confirm*: The password to use for the WebDAV login.

h5. Mission Planning

The first function of the GUI is to plan a mission for your ESP.  In order to do this, there are a couple of steps that need to be taken as initial setup so you can generate mission plans.  You must first create the instrument itself, and then you must define various protocols that can be placed in a mission plan.  First let's create a new instrument.  

# In the *ESP* drop down menu, select the *New Instrument...* option.
!ESPGUIFigure3.jpg|thumbnail,align=centre!
# A dialog window will appear that prompts you for the information about the ESP that you are using. In this example, we are using the ESP named 'Gordon' with a serial number of '1' and we chose a yellow color.  Click on 'Save' to save the information you entered.
{note:title=Instrument FTP not used yet}
Please note that while, in theory, you could use the GUI and point it to the FTP server on the instrument itself, it has not been implemented as there is some discussion about whether you would ever want to do that.  We use a shore station FTP server that keeps all the files in sync with the instrument itself and then point the GUI to that FTP server (this will be shown later).  For the time being, just leave all the FTP fields blank.
{note}
!ESPGUIFigure4.jpg|align=centre!
# Once you save the information, you will see your new instrument definition in the GUI.
!ESPGUIFigure5.jpg|thumbnail,align=centre!
# Now that the instrument is defined, we must define the various protocols that the instrument will be running.  To do this, click on the *ESP* menu and then select *Define Protocol...*.
!ESPGUIFigure6.jpg|thumbnail,align=centre!
This brings up a dialog where you can edit a new protocol that can be used in planning an ESP mission. 
!ESPGUIFigure7.jpg|align=centre!
In the figure, we have defined a new protocol with the name 'hab' and we chose a blue color so we can visually distinguish protocols on the calendar.  The default sample volume was chosen as 1000ml. The checkbox next to *Archive Volume* indicates that an archive should be performed after the protocol and it will use a sample volume of 500ml.  For mission planning purposes, it is good to define an approximate length (in minutes) that the protocol normally takes to run (in this case we chose 240 minutes).  The *Delay to Sample* field indicates the approximate amount of time it takes between when this protocol is started by the ESP and when the sample should actually start to draw water from the environment (in this case 5 minutes).  The *Initial Purge* checkbox tells the ESP to perform an initial purge when this protocol is run (selected in this case) and the *No Kill?* checkbox indicates if the kill step should be skipped (in this case the kill step is going to happen).
Remember that when you are defining a protocol in this step, you are defining a _template_ of the various protocols you will use to plan your mission.  When you actually plan your mission, you will be given an opportunity to customize each of these settings.
{note:title=Protocol Name is Critical}
The name that you assign to the protocol is REALLY important as that is the name that will be placed in the generated missions script and should match a protocol that has been defined in a ruby script on the machine.  For example, if there is a 'hab.rb' script on the ESP that you would like to use in your plans, make sure you define the protocol name as 'tab'.
{note}
# I did not go through each step here, but using this technique, I defined the following protocols
|| Name || Sample Volume || Archive Volume || Duration || Delay to Sample || Initial Purge || No Kill? || 
| hab | 1000 | 500 | 240 | 5 | (/) | |
| da | 1000 | nil | 300 | 7 | (/) | |
| habda | 1000 | 500 | 240 | 5 | (/) | |
| bac | 1000 | 500 | 200 | 3 | (/) | |
| larv | 1000 | 500 | 55 | 10 | (/) | |
| mfb | 500 | nil | 180 | 30 | (/) | |
| pcr | 1000 | 500 | 120 | 0 | (/) | |
{note:title=wcr created for you}
The ESP GUI will automatically create the archive protocol 'wcr' for you.
{note}
!ESPGUIFigure8.jpg|thumbnail,align=centre!
# Now we are ready to create a mission for the Gordon ESP.  Mouse of the instrument you want to create a mission for in the instrument window and right-click on it, then select *New Mission...*.
!ESPGUIFigure9.jpg|thumbnail,align=centre!
# This brings up a dialog window that allows you to fill in the information related to the mission that the ESP will be executing.
!ESPGUIFigure10.jpg|thumbnail,align=centre!
|| Field || Description || This Example ||
| Name | This is a user friendly name that you want to call you mission. One thing to note with this name and the instrument name is that the GUI will use the name of the instrument and the mission as a directory structure on your local machine to store local copies of all the files that the ESP produces/uses.  For example,  | In this example, we simply chose _JuanDeFuca_ |
| Latitude | This is the latitude where the ESP will be deployed | 43.031757 |
| Start Tube | This is the tube that will be used when this mission is started. | 2 |
| Longitude | This is the longitude where the ESP will be deployed | -126.752014 |
| Type | This is a drop down selection of a few available types of mission: Shallow, MFB, 1km, 4km | 4km |
| Depth | The depth at which the ESP will be deployed | 1000m |
| Start Date | This is the date and time of the start of the mission | 7/12/2011 09:42:44 |
| End Date | The date at which the mission will end | 8/31/2011 09:42:44 |
| FTP Hostname | This is the hostname of the FTP server which will host the files that the ESP is generating during its mission.  This FTP site is used to pull down the files to your local machine for analysis | bufflehead.shore.mbari.org |
| Mode | The mode the mission will be running in.  This is most likely "real", but there are "Simfast", "Simreal", and "Quick" modes as well | real |
| FTP Root | This is the base directory on the FTP server where the ESP will be recording it's files.  This is usually where the log file is located. | In this example, the complete FTP URL to the data is: _ftp://bufflehead.shore.mbari.org/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_ which means the host is _buffelhead.shore.mbari.org_ and the FTP Root is _/ESP/2011/EPS_Deployments/JuanDeFuca2011/Gordon_var_log2011aug25/:95H4700_.  A sample of what the directory contents for a mission might look like, see the figure below.
!ESPGUIFigure11.jpg|thumbnail,align=centre!
| Home Path | Not used | |
| FTP Username | This is the username that will be used to connect to the FTP server | anonymous |
| Config Path | Not used | |
| FTP Password | This is the password that will be used to connect to the FTP server | |
| Log Path | This is the path on the ESP itself where the files are begin written (images, real.log, .pcr, etc.).  This is used by the GUI when it parses the log file looking for information as it needs to know where to find files in the FTP structure. | /var/log/esp |
| Log File | This is the name of the file that is being written to by the ESP during its operation | real.log |
| Path | Not used | |
When all the information is filled out, click on "Save" to save the mission.
# In the instruments window, if you now click on the arrow to the left of the instrument (Gordon) you will see a tree view with your new mission listed below.
# Click on the check box next to the mission (JuanDeFuca) to bring the mission into view in the Calendar Window.
!ESPGUIFigure12.jpg|thumbnail,align=centre!
# Now it is time to add some protocols to your mission!  If you right click on the calendar at the approximate time that the protocol is to run, you will get a context menu that will allow you to select the protocol you will to insert into the mission.  In the figure below, we are adding a "bac" protocol in the afternoon of the 19th of July.
!ESPGUIFigure13.jpg|thumbnail,align=centre!
# This brings up a dialog to allow you to edit specific information about this protocol run.
!ESPGUIFigure14.jpg|align=centre!
# I changed the name to something meaningful to me and then changed the time, sample volume and archive volume to match what I wanted for this particular run of the bac protocol.  Then click on "Save" to save the protocol in the mission.
!ESPGUIFigure15.jpg|thumbnail,align=centre!
# I used the same method to add 5 more protocols to the mission plan as an example.
!ESPGUIFigure16.jpg|thumbnail,align=centre!
# Once you have the mission the way you like it, you can generate the ruby script that will execute the mission on the ESP by right-clicking on either the mission in the Calendar Window or in the Instrument List Window and selecting "Generate Script...".
!ESPGUIFigure17.jpg|thumbnail,align=centre!
# This opens a window that displays the script and gives you and option to save it to your local disk somewhere (click on "Save Script...") to do this.
!ESPGUIFigure18.jpg|align=centre!

h5. Data Management and Analysis

Once your mission is underway, the ESP GUI can be used to look at and analyze the data that the ESP is generating.  Once the ESP starts generating logs, images and files, you should see them show up in the FTP site that you defined in the mission planning portion above.  Continuing with that example, if I start the GUI, expand the arrow next to "Gordon" and then select the checkbox next to the "JuanDeFuca" mission, it will appear in the calendar view. With that selected, let's look a little closer at the ESP and Mission Tabs Window.  If you click on the "ESP" table you will see a short table with the information about the ESP that is running the mission you are examining (in this case, Gordon).
!ESPGUIFigure19.jpg|thumbnail,align=centre!
If you select the "Planned" tab, you will see a tabular view of the various protocols that you defined in the mission planning phase.
!ESPGUIFigure20.jpg|thumbnail,align=centre!
You can select the "Actual" tab, but will not see anything yet as we have not parsed the log file from the ESP to see what has actually happened out there.  The same goes for "Samples", "Images" and "Ancillary".  Nothing will show in these tabs until the GUI has had an opportunity to parse the information out of the log file that the ESP generates.  Which brings us to the "Files" tab.
!ESPGUIFigure21.jpg|thumbnail,align=centre!
The Files tab is a tree view of the combination of the files both in your local directory and on the remote FTP server. In this case what you can see is that all of the files listed here are available on the remote server but not on your local disk drive. This is indicated by the icon having red bar on the bottom.  If the icon has a green bar only it is both on the remote server and on your local disk and the two are in sync.  If the icon has a green bar and two small arrows it means that the file is located both on your disk and on the remote server, but they are out of sync and in need of a re-sync.  If the icon has no color on it, it is on your local disk and not on the remote server and nothing needs to be done. Let's examine what your options are at this point.
!ESPGUIFigure22.jpg|align=centre!
]]></property>
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<id name="id">18285063</id>
<property name="body"><![CDATA[# [Spring 2010|^ESP G3 project overview.doc|first pass FR for G3]
# [Nov, 2010|^ESP G3 project requirements.doc|second pass FR for G3]
# [Sept 15, 2011|^Funct Req Sept 15 2011.docx|third pass FR for G3]]]></property>
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<id name="id">18285117</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

|| Event || Example || Rule Used || Information Parsed ||
| Mission Start | {noformat}."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"{noformat} |{noformat}"^GoodNews\\.\\S+\\s+\\\"Starting\\s+w/pucks\\s+in\\s+tube\\s+(\\d+).*Subject=>\\\"(\\S+)\\s+begun\\\".*"{noformat} | # Starting tube
# Mission name |
| Ancillary Data | {noformat}#\Can@13:19:34, 48.2V, 17.3C, 44% humidity, 14.5psia, 14.84V, 0.42A, 0.413A avg, 6.21W
CTD@13:24:25, 3.3694C, 999.623 decibars, 3.1914 S/m, 104.61%, -0.180 1/m, 0.33 ml/l, 3.0760C
ISUS@13:24:45, 24.460 uM/L no^3, -1.000 uM/L hs, 22.7800psu{noformat} | # First it removes all newlines from the log entry and then checks to see if the entry may have ancillary data by using the pattern {no format}"^Can@.*"{no format}
# If it matches, then it takes the original log entry, splits it by newlines (I replace '\' with newlines earlier in the process) and then pattern match each line with {no format}"^(\\S+)@(\\d\\d):(\\d\\d):(\\d\\d),(.*)$"{no format} to search for time, source and the payload of the message. | # Source
# Time
# Payload | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

|| Event || Example || Rule Used || Information Parsed ||
| Mission Start | {noformat}."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"{noformat} |{noformat}"^GoodNews\\.\\S+\\s+\\\"Starting\\s+w/pucks\\s+in\\s+tube\\s+(\\d+).*Subject=>\\\"(\\S+)\\s+begun\\\".*"{noformat} | # Starting tube
# Mission name |
| Ancillary Data | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

|| Event || Example || Rule Used || Information Parsed ||
| Mission Start | {noformat}."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"{noformat} |{noformat}"^GoodNews\\.\\S+\\s+\\\"Starting\\s+w/pucks\\s+in\\s+tube\\s+(\\d+).*Subject=>\\\"(\\S+)\\s+begun\\\".*"{noformat} | # Starting tube
# Mission name |
| Ancillary Data | {noformat}#\Can@13:19:34, 48.2V, 17.3C, 44% humidity, 14.5psia, 14.84V, 0.42A, 0.413A avg, 6.21W
CTD@13:24:25, 3.3694C, 999.623 decibars, 3.1914 S/m, 104.61%, -0.180 1/m, 0.33 ml/l, 3.0760C
ISUS@13:24:45, 24.460 uM/L no^3, -1.000 uM/L hs, 22.7800psu{noformat} | # First it removes all newlines from the log entry and then checks to see if the entry may have ancillary data by using the pattern {noformat}"^Can@.*"{noformat}
# If it matches, then it takes the original log entry, splits it by newlines (I replace '\' with newlines earlier in the process) and then pattern match each line with {noformat}"^(\\S+)@(\\d\\d):(\\d\\d):(\\d\\d),(.*)$"{noformat} to search for time, source and the payload of the message. | # Source
# Time
# Payload | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

|| Event || Example || Rule Used || Information Parsed ||
| Mission Start | {noformat}."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"{noformat} |{noformat}^GoodNews\\.\\S+\\s+\\\"Starting\\s+w/pucks\\s+in\\s+tube\\s+(\\d+).*Subject=>\\\"(\\S+)\\s+begun\\\".*{noformat} | # Starting tube
# Mission name |
| Ancillary Data | {noformat}#\Can@13:19:34, 48.2V, 17.3C, 44% humidity, 14.5psia, 14.84V, 0.42A, 0.413A avg, 6.21W
CTD@13:24:25, 3.3694C, 999.623 decibars, 3.1914 S/m, 104.61%, -0.180 1/m, 0.33 ml/l, 3.0760C
ISUS@13:24:45, 24.460 uM/L no^3, -1.000 uM/L hs, 22.7800psu{noformat} | # First it removes all newlines from the log entry and then checks to see if the entry may have ancillary data by using the pattern {noformat}^Can@.*{noformat}
# If it matches, then it takes the original log entry, splits it by newlines (I replace '\' with newlines earlier in the process) and then pattern match each line with {noformat}^(\\S+)@(\\d\\d):(\\d\\d):(\\d\\d),(.*)${noformat} to search for time, source and the payload of the message. | # Source
# Time
# Payload | 
| Process Run Start with Archive | {noformat}#pcr sampling at most 1000ml, wcr at most 1000ml{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml, wcr at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume
# Archive Target Volume | 
| Process Run Start without Archive  | {noformat}{noformat} | {noformat}^(.+) sampling at most (\\d+\\.*\\d*)ml{noformat} | # Process run name
# Process Run Target Volume | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 
|  | {noformat}{noformat} | {noformat}{noformat} | | 

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

|| Event || Log Entry || Rule Used || Information Parsed ||
| Mission Start | {noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat} |{noformat}"^GoodNews\\.\\S+\\s+\\\"Starting\\s+w/pucks\\s+in\\s+tube\\s+(\\d+).*Subject=>\\\"(\\S+)\\s+begun\\\".*"{noformat} | # Starting tube
# Mission name |

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

|| Event || Log Entry || Rule Used || Information Parsed ||
| Mission Start | {noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat} | | |

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<property name="body"><![CDATA[h2. Below are links to attached Word Documents

# [Spring 2010|^ESP G3 project overview.doc|first pass FR for G3]
# [Nov 11, 2010|^ESP G3 project requirements.doc|second pass FR for G3]
# [Sep 15, 2011|^Funct Req Sept 15 2011.docx|third pass FR for G3]
# [Sep 21, 2011|^Funct Req Sept 21 2011.docx|fourth pass FR for G3]]]></property>
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<property name="body"><![CDATA[h2. Below are links to attached Word Documents

# [Spring 2010|^ESP G3 project overview.doc|first pass FR for G3]
# [Nov 11, 2010|^ESP G3 project requirements.doc|second pass FR for G3]
# [Sep 15, 2011|^Funct Req Sept 15 2011.docx|third pass FR for G3]]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
\\
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage taken by Rob Vincent:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]

Map of locations:&nbsp; [http://maps.google.com/maps/ms?ie=UTF&msa=0&msid=213220825771739778963.0004a40bdd601babc291d]

May 23.&nbsp; Attempted recovery of ESP.&nbsp; Message from Roman:

{color:#996600}&nbsp;&nbsp;&nbsp; We went out to the site where espbruce was moored and attempted to find it.&nbsp; The weather was very poor and water was very turbid.&nbsp; Using the ships depth finder we found a promising target.&nbsp; In difficult conditions the divers performed a search but espbruce was not found.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; We recovered the mooring.&nbsp; It looks like the cable was pulled straight out of the cone.&nbsp; The top mast is bent but I cannot say if this was caused by a rough landing on the beach or boat impact.&nbsp; There are no dents or gouges on the mooring.&nbsp; The radio box is dry and antenna looks ok.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; Thursday the RV Gulf Challenger may be able to survey the area with a side scanning sonar.&nbsp; This will be a much better way to search for espbruce.&nbsp;{color}

Message from Roman May 26:

{color:#996600}&nbsp;&nbsp;&nbsp; ESPbruce was located at&nbsp; 43° 02.0740 N&nbsp;&nbsp; 70° 36.8447 W at ~ 10m depth.&nbsp; This position is about 19 yards from the waypoint.&nbsp; So looks like it wasn't dragged and has maintained seal integrity.&nbsp; We will attempt to recover it this weekend if we can get the RV Tioga.&nbsp; If not will recover with the RV Connecticut on june 7th weather permitting.{color}
&nbsp;

Dates for a recovery kept moving as weather and scheduling problems arose.&nbsp; Finally, Roman reported on June 15:
{quote}
{quote}
{color:#996600}ESPbruce was recovered today with no visible external damage. The EM cable strain relief is still on the cable.&nbsp; The recovery operation used two ships the RV Gulf Challenger and it's sister the RV Tioga.&nbsp; The Challenger supported the the side scan survey and the Tioga supported the divers and lifting of the core package and its anchor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;The side scan sonar operator advised me at the beginning of the day that he believed the esp package would be found on the bottom.&nbsp; He based this opinion on the data secured by his colleague almost two weeks ago.&nbsp; From his read of that run, he believed that the instrument was 15m off the bottom at that time.&nbsp; Depth at this site is 49m.&nbsp; He felt that the instrument was slowly sinking and that by today it was surly be on the sea floor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Todays side scan survey took approximately 90 minutes.&nbsp; They had acquired a strong signature on the core and calculated that it was at a depth of 65 feet (~20m). The package&nbsp; was still located within 10m of the original deployment site.&nbsp; They dropped a marker line with a float as close to the calculated position as possible.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;At this point divers equipped with twin 80 cu ft Nitrox cylinders and electric scooters dived on the marker.&nbsp; They had 70 minutes of search time.&nbsp; After 42 minutes an orange sausage float attached to a spectra lift line appeared.&nbsp; Then 10 minutes later a second lift bag attached to the EM cable appeared.&nbsp; The divers surfaced after a total bottom time of 62 minutes.&nbsp; Eight minutes to spare.&nbsp; We recovered the divers.&nbsp; They reported that the depth of top of the can was at 26 feet (~8m) right where it was supposed to be.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Recovery went smoothly using a single winch equipped with a capstan attachment.&nbsp; By alternately shifting the load from drum (used to lift anchor) and capstan (used to lift instrument we recovered the package and the anchor safely.{color}
{quote}
\\
\\  {color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford.

{color:#cc3300}July 6{color} \-\- Ship by truck D-ESP and supplies for JdF cruise.&nbsp; To Newport, OR.

{color:#cc3300}July 13{color} \-\- Sail for Axial and JdF (1 day late due to weather getting up to Newport)

{color:#cc0000}July 20{color} \-\- recall D-ESP.&nbsp; Recover all instruments.&nbsp; Two more days for Dave Clague.&nbsp; Ship returns July 23.
\\

Aug 17 \-\- Matson picks up loaded ESP van.&nbsp; Genset on truck putting out >530V so our reefer unit will not start.&nbsp; Decide to send due to late hour and ship leaving tomorrow.&nbsp; Van wt. w/ all ESP-Drifter gear: 15,000 lbs.]]></property>
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<property name="body"><![CDATA[h2. Overview

h2. Notes

The printer used by [~scholin] is a custom printer. It can not output GAL files. It does put out a text file that I'm trying to parse and work with. A copy of the file is checked into [SVN|http://kahuna.shore.mbari.org/viewvc.cgi/esp/trunk/esp-imaging/src/test/resources/imaging/2_22_08comptest_2008-02-25_142348_Run.txt?view=markup].

h3. Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:
{noformat}
SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK
{noformat}

_SpotX_ and _SpotY_ are coordinates in micrometers starting in the upper left hand corner of the paper. The _0, 0_ point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out.

_SrcWell_ indicates the contents of the spots. For example, all spots from the _C-1_ source well will have identical chemistries applied.

h3. Image Analysis

Maximum Entropy thresholding does a decent job of delineating the control spots. Unfortunately, I haven't found a technique for delineating the spots that don't go off. In fact those spots can contain values with in the range of the background noise. 

h4. Possible avenues of exploration

The ESP folks would like an automated image analysis package that:
# Reads the image
# locates the spots (either with or without the help of the GAL-like file)
# Read the highest 8x8 block (full size image) or 4x4 block (half-size image) average within the spot. The block average is square with no weighting applied.
# Return a text file (Tab or comma delimited) with:
#* Average intensity associated with the _SrcWell_ (i.e. C-1, A-1, etc.)
#* Standard deviation by _SrcWell_
#* Average intensity of background disk (excluding spot values)

{gallery}

h3. References
# Old ESP Matlab toolbox at [http://moonjelly/cgi-bin/cvsweb.cgi/ESP/matlab/]
]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">3179952</id>
<property name="body"><![CDATA[h2. Overview

h2. Notes

The printer used by [~scholin] is a custom printer. It can not output GAL files. It does put out a text file that I'm trying to parse and work with. A copy of the file is checked into [SVN|http://kahuna.shore.mbari.org/viewvc.cgi/esp/trunk/esp-imaging/src/test/resources/imaging/2_22_08comptest_2008-02-25_142348_Run.txt?view=markup].

h3. Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:
{noformat}
SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK
{noformat}

_SpotX_ and _SpotY_ are coordinates in micrometers starting in the upper left hand corner of the paper. The _0, 0_ point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out.

_SrcWell_ indicates the contents of the spots. For example, all spots from the _C-1_ source well will have identical chemistries applied.

h3. Image Analysis

Maximum Entropy thresholding does a decent job of delineating the control spots. Unfortunately, I haven't found a technique for delineating the spots that don't go off. In fact those spots can contain values with in the range of the background noise. 

{gallery}

h4. Possible avenues of exploration

The ESP folks would like an automated image analysis package that:
# Reads the image
# locates the spots (either with or without the help of the GAL-like file)
# Read the highest 8x8 block (full size image) or 4x4 block (half-size image) average within the spot. The block average is square with no weighting applied.
# Return a text file (Tab or comma delimited) with:
#* Average intensity associated with the _SrcWell_ (i.e. C-1, A-1, etc.)
#* Standard deviation by _SrcWell_
#* Average intensity of background disk (excluding spot values)


h3. References
# Old ESP Matlab toolbox at [http://moonjelly/cgi-bin/cvsweb.cgi/ESP/matlab/]
]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">3179947</id>
<property name="body"><![CDATA[h2. Overview

h2. Notes

The printer used by [~scholin] is a custom printer. It can not output GAL files. It does put out a text file that I'm trying to parse and work with. A copy of the file is checked into [SVN|http://kahuna.shore.mbari.org/viewvc.cgi/esp/trunk/esp-imaging/src/test/resources/imaging/2_22_08comptest_2008-02-25_142348_Run.txt?view=markup].

h3. Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:
{noformat}
SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK
{noformat}

SpotX and SpotY are coordinates in micrometers starting in the upper left hand corner of the paper. The _0, 0_ point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out

h3. Image Analysis

Using ImageJ, it's possible to locate the spots using _Plugins -> Filters -> MultiThresholder_ (Select _Maximum Entropy_ in the Dialog). To do this in a program we would need to include both the {{ij.jar}} and {{plugin/Filters/Multi_thresholder.jar}}

{gallery}

h3. References
# Old ESP Matlab toolbox at [http://moonjelly/cgi-bin/cvsweb.cgi/ESP/matlab/]
]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">3114475</id>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">3179949</id>
<property name="body"><![CDATA[h2. Overview

h2. Notes

The printer used by [~scholin] is a custom printer. It can not output GAL files. It does put out a text file that I'm trying to parse and work with. A copy of the file is checked into [SVN|http://kahuna.shore.mbari.org/viewvc.cgi/esp/trunk/esp-imaging/src/test/resources/imaging/2_22_08comptest_2008-02-25_142348_Run.txt?view=markup].

h3. Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:
{noformat}
SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK
{noformat}

_SpotX_ and _SpotY_ are coordinates in micrometers starting in the upper left hand corner of the paper. The _0, 0_ point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out.

_SrcWell_ indicates the contents of the spots. For example, all spots from the _C-1_ source well will have identical chemistries applied.

h3. Image Analysis

Using ImageJ, it's possible to locate the spots using _Plugins -> Filters -> MultiThresholder_ (Select _Maximum Entropy_ in the Dialog). To do this in a program we would need to include both the {{ij.jar}} and {{plugin/Filters/Multi_thresholder.jar}}

{gallery}

h3. References
# Old ESP Matlab toolbox at [http://moonjelly/cgi-bin/cvsweb.cgi/ESP/matlab/]
]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">3114477</id>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">3179950</id>
<property name="body"><![CDATA[h2. Overview

h2. Notes

The printer used by [~scholin] is a custom printer. It can not output GAL files. It does put out a text file that I'm trying to parse and work with. A copy of the file is checked into [SVN|http://kahuna.shore.mbari.org/viewvc.cgi/esp/trunk/esp-imaging/src/test/resources/imaging/2_22_08comptest_2008-02-25_142348_Run.txt?view=markup].

h3. Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:
{noformat}
SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK
{noformat}

_SpotX_ and _SpotY_ are coordinates in micrometers starting in the upper left hand corner of the paper. The _0, 0_ point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out.

_SrcWell_ indicates the contents of the spots. For example, all spots from the _C-1_ source well will have identical chemistries applied.

h3. Image Analysis

Maximum Entropy thresholding does a decent job of delineating the control spots. Unfortunately, I haven't found a technique for delineating the spots that don't go off. In fact those spots can contain values with in the range of the background noise. 

h4. Possible avenues of exploration

The ESP folks would like an automated image analysis package that:
# Reads the image
# locates the spots (either with or without the help of the GAL-like file)
# Read the highest 8x8 block (full size image) or 4x4 block (half-size image) average within the spot. The block average is square with no weighting applied.
# Return a text fiel (Tab ro comma delimited) with:
#* Average intensity associated with the _SrcWell_ (i.e. C-1, A-1, etc.)
#* Standard deviation by _SrcWell_
#* Average intensity of background disk (excluding spot values)

{gallery}

h3. References
# Old ESP Matlab toolbox at [http://moonjelly/cgi-bin/cvsweb.cgi/ESP/matlab/]
]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began?? and ended ~ week later when pump tore from piling.

*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).
Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays
Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

MELO used was #300034012090780

location reported by MELO was-\- &nbsp; 33.4865 \-118.51285

*March 20*\--lost comms

*March 21*\--re-established comms and think problem in E/M cable.

*March 22*\--lost comms

*April 3*\--small boat to buoy to test E/M cable

*April 8*\--'rescue' mission. Swapped E/M cables and repositioned in slightly deeper water, at 33.48504 \-118.50988

water depth 175m.&nbsp; top of can 10.9m


*May 1*\--mission ended and mooring recovered.

h4. {color:#ff00cc}ECOHAB--S. California{color}

*April 1*\--Instruments deployed

&nbsp;MOE--inshore at 33.60779 \-118.01877 with ISUS

Melo was 300234060014550

avg can depth \~9m
\\

&nbsp;Bruce--offshore at 33.58609 \-118.03686

Melo was 300234060016190

avg can depth \~19.5m

*~ April 9* lost communication with Bruce.&nbsp;

*April 15*\--Rescue mission w/Nerissa found 'hung' modem.&nbsp; Power cycled and checked cables on deck.&nbsp; Re-deployed in nearby spot.&nbsp; Divers (Kim R. & George M) measured 17.7m to top of can, 25.3 m to master link.

*May 2*\--Mission ended and recovered both instruments ]]></property>
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<property name="body"><![CDATA[# [Notes from delivery of 3rd module (April 1, 2009)]
# [Module 07 checkout notes (May 22, 2009)|^pcrmodule_checkout_20090522.xls]
# [LLNL/Spyglass meeting 29Oct2009]]]></property>
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<property name="body"><![CDATA[h2. For discussion:


h3. Tech Transfer

* Bruce update

h3. MFB

* AIV hole sizes; what should we order?

h3. Software


h3. Sphere and 4K DWSMS


h3. GUI Development]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[# [Notes from delivery of 3rd module (April 1, 2009)]
# [Module 07 checkout notes (May 22, 2009)|^pcrmodule_checkout_20090522.xls]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10911884</id>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.3|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.3%2028_12_2007.doc]
# [PCR Users Manual v1.0|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20PCR%20Module%20Users%20Manual%20V1.0.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram12-19-07.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10944644</id>
<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision
# [25Jun2009]
# 02Jul2009 - no meeting; 4th of July break
# [09Jul2009]
# [16Jul2009]
# [23Jul2009]
# 30Jul2009 - Scott ran mtg; proposal preparation
# [06Aug2009]
# 13Aug2009 - cancelled; proposal/grant preparations
# [20Aug2009]
# 27Aug2009 - Jim Vacation; Scott in charge
# 03Sep2009 - Jim Vacation; Scott in charge
# [10Sep2009]
# [01Oct2009]
# [08Oct2009]
# [15Oct2009]
# [22Oct2009]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.3|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.3%2028_12_2007.doc]
# [PCR Users Manual v1.0|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20PCR%20Module%20Users%20Manual%20V1.0.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram 04-07-08.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.3|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.3%2028_12_2007.doc]
# [PCR Users Manual v1.0|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20PCR%20Module%20Users%20Manual%20V1.0.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram 04-07-08.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.3|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.3%2028_12_2007.doc]
# [PCR Users Manual v1.0|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20PCR%20Module%20Users%20Manual%20V1.0.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram4-07-08.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.3|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.3%2028_12_2007.doc]
# [PCR Users Manual v1.0|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20PCR%20Module%20Users%20Manual%20V1.0.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram04-07-08.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[Present: Cheri,  Doug, Brent, Jim, Scott, Chris S., Chris P., Roman

h3. Machine Builds

* &nbsp;

h3. MFB&nbsp;


h3. Drifter


h3. Software


h3. Deep ESP/DWSM


h3. GUI


h3. Deployment Issues


h3. &nbsp;Other Items]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision
# [25Jun2009]
# 02Jul2009 - no meeting; 4th of July break
# [09Jul2009]
# [16Jul2009]
# [23Jul2009]
# 30Jul2009 - Scott ran mtg; proposal preparation
# [06Aug2009]
# 13Aug2009 - cancelled; proposal/grant preparations
# [20Aug2009]
# 27Aug2009 - Jim Vacation; Scott in charge
# 03Sep2009 - Jim Vacation; Scott in charge
# [10Sep2009]
# [01Oct2009]
# [08Oct2009]
# [15Oct2009]
# [22Oct2009]
# 29Oct2009 - Jim LLNL;Engineering & Chris set-up schedule for next MARS
# [05Nov2009] \-meeting of all ESP team on 03Nov]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision
# [25Jun2009]
# 02Jul2009 - no meeting; 4th of July break
# [09Jul2009]
# [16Jul2009]
# [23Jul2009]
# 30Jul2009 - Scott ran mtg; proposal preparation
# [06Aug2009]
# 13Aug2009 - cancelled; proposal/grant preparations
# [20Aug2009]
# 27Aug2009 - Jim Vacation; Scott in charge
# 03Sep2009 - Jim Vacation; Scott in charge
# [10Sep2009]
# [01Oct2009]
# [08Oct2009]
# [15Oct2009]
# [22Oct2009]
# 29Oct2009 - Jim LLNL;Engineering & Chris set-up schedule for next MARS
# [05Nov2009] -meeting all ESP on 03Nov]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]<--\-{color:#ff0000}{*}NEW (Oct 7, 2009{*}{color})
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [Functional Requirements for Gen 3 ESP]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB 2007-08 Timeline |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.7|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1_7%2010_03_2008.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/Fluidics_worksheet_04Dec08.pdf]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

*Dec 2, 2013*\--Fired off final sample.&nbsp; Recover slated for Dec 11, 2013. Ran a total of 24 samples, each with an archive.

*Dec 11, 2013*\--Successful recovery.&nbsp; Sable never fired, and significant corrosion around ISMS intake, but overall looks very clean.


h4. {color:#ff00cc}Puget Sound{color}

_{+}Lummi Bay:+_

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)

*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.&nbsp; Subsequent investigation found that modem card had been cancelled with T-Mobile due to NOAA miscommunication.&nbsp; When new one was tried, operator did not know to 'close the door' on the modem in order to power the card.&nbsp; Brent flew up and fixed.&nbsp; Missed 4 days of sampling.

*August 18*\--Lummi Bay deployment ended.&nbsp; Machine returned to NOAA.

_{+}Samish Bay:&nbsp;+_

*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; No CTD.&nbsp; Both machines have MFB and PCR.&nbsp; Media event was July 18.

Aug 14--Recover Gordon

Aug 17--Deploy (swap) NEO.

Sep 10--processing syringe servo motor has failed.&nbsp; Decision to run out remaining mission with archive only.

*Sep 16*\--NEO's mission ends.&nbsp; NOAA to recover and Roman/Kevan retrieved both machines Sep 25.

h4. {color:#ff00cc}ECOHAB/CANON--Monterey Bay{color}

*&nbsp;September 10, 2013*\-\- Deploy 2 ESP's in Monterey Bay.&nbsp; First time in southern part of bay.
\\

{color:#cc3366}*'North'*{color}
ESP-Mack.&nbsp; Lat 36.9048, Long \-121.93659, Water depth 32m, Can depth 9.8m.

*Oct 11, 2013*\--Battery voltage dropped too low, and we had to end mission

{color:#cc3366}*'South'*{color}
ESP-Bruce. Lat 36.63908, Long \-121.87884, Water depth 60m, Can depth 4.8m

*Oct 10, 2013*\-Found 'terminal fluid retention' on processing side-pulled an oring or some type of leak. Tried porting waste to Waste2 (known to be empty), but same results.  Final 3 samples to try and collect for SEM work.
\\

*October 21, 2013* \-\- Recovered both instruments]]></property>
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<property name="body"><![CDATA[Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note that we have yet to make a full batch of high-volume snap pucks, but when we do, those will be labeled 1HV (top and bottom).

Here is who is doing our etching:

LaserMark
2109 O'Toole Ave. Ste S
San Jose, CA 95131
Phone 408 433-9333
Fax 408 433-9343 \\ \\

Here is what I have packed up for etching:
| Type | Top/bottom | Numbered | Amount | NOTE |
| WCR | Top | 040-079 | 40 | \\ |
| \\ | Bottom | 040-079 | 40 | \\ |
| LAF | Top | 040-078 | 39 | 1=Missing |
| \\ | Bottom | 040-078 | 39 | 1=Missing |
| SAF | Top | 040-075 | 36 | 4sent to Gregg D |
| \\ | Bottom | 040-075 | 36 | 4sent to Gregg D |
| SHT | Top | 080-159 | 80 | \\ |
| SH1 | Bottom | 080-159 | 80 | \\ |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 390 | \\ |
\\ \\

I also sent 1 WCR puck (top&bottom) as a font sample.&nbsp; When these come back I will pack up the ones that are to be re-numbered(SHT2000-079).&nbsp; I haven't received a quote yet but Laser Mark said about $2 each piece + shipping.]]></property>
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<property name="body"><![CDATA[These are documents]]></property>
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<property name="body"><![CDATA[# Requirements
]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://predator.shore.mbari.org/esp_gui/launch.jnlp]

h3. Project Documentation:

h3. Other Documents
# [Documents|ProjectDocuments]
# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
## [ESP GUI Demo and Questions|2007_09_05]
## [Follow up meeting on Resources and Consumables|2008_01_08]
## [Mock Mission Planning Meeting|2008_03_11]
# [Presentations|ProjectPresentations]
# [Data Model]
# [Developer Documentation]

h3. Bug Tracking
# [JIRA Issue Tracker|http://oceana.shore.mbari.org:8082/browse/ESPII]

]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://predator.shore.mbari.org/esp_gui/launch.jnlp]

h3. Project Documentation:

h3. Other Documents
# [Documents|ProjectDocuments]
# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
## [ESP GUI Demo and Questions|2007_09_05]
## [Follow up meeting on Resources and Consumables|2008_01_08]
## [Mock Mission Planning Meeting|2008_03_11]
# [Presentations|ProjectPresentations]
# [Tasks]
# [Data Model]
# [Developer Documentation]

h3. Bug Tracking
# [JIRA Issue Tracker|http://oceana.shore.mbari.org:8082/browse/ESPII]

]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://predator.shore.mbari.org/esp_gui/launch.jnlp]

h3. Project Documentation:

h3. Other Documents
# [Documents|ProjectDocuments]
# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
## [ESP GUI Demo and Questions|2007_09_05]
## [Follow up meeting on Resources and Consumables|2008_01_08]
## [Mock Mission Planning Meeting|2008_03_11]
# [Presentations|ProjectPresentations]
# [Tasks]
# [Data Model]
# [Developer Documentation]

h3. Bug Tracking
# [JIRA Issue Tracker|http://oceana.shore.mbari.org:8082/browse/ESPAPP]

]]></property>
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<property name="body"><![CDATA[# The user cannot change the make up of a phase once it has been defined.  If the sequence or timing of the contents of a phase changes, a new phase must be created.]]></property>
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<property name="body"><![CDATA[# Do we need to track the serial numbers of the pucks in the application?
]]></property>
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<property name="body"><![CDATA[# The user cannot change the make up of a phase once it has been defined.  If the sequence or timing of the contents of a phase changes, a new phase must be created.
# The combination of the phase identifier and the protocol identifier is a "unique key" in determining how much of the various consumables will be used.]]></property>
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# [Terminology]
# [Outstanding Questions]
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# [Terminology]]]></property>
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<property name="body"><![CDATA[# [Requirements]
]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound.

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
\\]]></property>
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<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically (colors are same deployment)+

{color:#ff00ff}April 6--Bruce at M0 for surface deployment (Zephyr){color}

April 15--Mack in Sphere (dive #1) for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in Sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

{color:#ff00ff}April 29--Recover Bruce at M0 (Zephyr){color}

May 1--Mack in Sphere (dive #3) connected to DWSM; incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

{color:#0033cc}May 14--Deploy NEO w/PCR, surface deployment (Zephyr){color}

May 27--First Drifter dive; used weighted cable (Zephyr)

June 5-9 \-\- Western Flyer Trip.&nbsp; D-ESP, Drifter, and CTD casts. {color:#cc0000}{*}MOVIES{*}{color}:  D-ESP launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/DESP%20deployment%20(full%20quality).dv].  Drifter launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/Drifter.dv].

{color:#0033cc}June 11 \-\- Recover NEO.&nbsp; (Zephyr){color}\\

+FALL Network Deployment+

Proposed locations are here: [http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&msid=113879459163411006053.000471828af997bd7d89c&t=h&z=12]

September 24 \-\- Deploy Moe w/PCR at M0.&nbsp; Deployed Mack at Santa Cruz.&nbsp; {color:#66cc00}Deployed Bruce in the bight.&nbsp; (Zephyr)&nbsp; Lost communications with Bruce that day.{color}

{color:#66cc00}September 28 \-\- Recover (dead) Bruce.&nbsp; Comms box had water in it, but radio worked.&nbsp; EM cable had 2 broken wires. (Zephyr){color}

September 30 \-\- Deploy D-ESP on MARS (Lobos).&nbsp; Hand issue at first, but 'fixed' itself.&nbsp; Worked until Oct. 7 when wrong puck was loaded and water introduced into core, frying puck heater.&nbsp; We turned off and first recovery day (Oct 13) is weathered out.&nbsp; It still awaits recovery.

{color:#66cc00}October 14 \-\- Re-deploy Bruce (Zephyr).&nbsp; New comms box, re-terminated EM cable.&nbsp; Working well after deployment.{color}

October 20 \-\- Install pump system on pier at Santa Cruz Wharf.&nbsp; Neo to be installed and start running Oct 22. ]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
\\
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage taken by Rob Vincent:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]

Map of locations:&nbsp; [http://maps.google.com/maps/ms?ie=UTF&msa=0&msid=213220825771739778963.0004a40bdd601babc291d]

May 23.&nbsp; Attempted recovery of ESP.&nbsp; Message from Roman:

{color:#996600}&nbsp;&nbsp;&nbsp; We went out to the site where espbruce was moored and attempted to find it.&nbsp; The weather was very poor and water was very turbid.&nbsp; Using the ships depth finder we found a promising target.&nbsp; In difficult conditions the divers performed a search but espbruce was not found.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; We recovered the mooring.&nbsp; It looks like the cable was pulled straight out of the cone.&nbsp; The top mast is bent but I cannot say if this was caused by a rough landing on the beach or boat impact.&nbsp; There are no dents or gouges on the mooring.&nbsp; The radio box is dry and antenna looks ok.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; Thursday the RV Gulf Challenger may be able to survey the area with a side scanning sonar.&nbsp; This will be a much better way to search for espbruce.&nbsp;{color}

Message from Roman May 26:

{color:#996600}&nbsp;&nbsp;&nbsp; ESPbruce was located at&nbsp; 43° 02.0740 N&nbsp;&nbsp; 70° 36.8447 W at ~ 10m depth.&nbsp; This position is about 19 yards from the waypoint.&nbsp; So looks like it wasn't dragged and has maintained seal integrity.&nbsp; We will attempt to recover it this weekend if we can get the RV Tioga.&nbsp; If not will recover with the RV Connecticut on june 7th weather permitting.{color}
&nbsp;

Dates for a recovery kept moving as weather and scheduling problems arose.&nbsp; Finally, Roman reported on June 15:
{quote}
{quote}
{color:#996600}ESPbruce was recovered today with no visible external damage. The EM cable strain relief is still on the cable.&nbsp; The recovery operation used two ships the RV Gulf Challenger and it's sister the RV Tioga.&nbsp; The Challenger supported the the side scan survey and the Tioga supported the divers and lifting of the core package and its anchor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;The side scan sonar operator advised me at the beginning of the day that he believed the esp package would be found on the bottom.&nbsp; He based this opinion on the data secured by his colleague almost two weeks ago.&nbsp; From his read of that run, he believed that the instrument was 15m off the bottom at that time.&nbsp; Depth at this site is 49m.&nbsp; He felt that the instrument was slowly sinking and that by today it was surly be on the sea floor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Todays side scan survey took approximately 90 minutes.&nbsp; They had acquired a strong signature on the core and calculated that it was at a depth of 65 feet (~20m). The package&nbsp; was still located within 10m of the original deployment site.&nbsp; They dropped a marker line with a float as close to the calculated position as possible.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;At this point divers equipped with twin 80 cu ft Nitrox cylinders and electric scooters dived on the marker.&nbsp; They had 70 minutes of search time.&nbsp; After 42 minutes an orange sausage float attached to a spectra lift line appeared.&nbsp; Then 10 minutes later a second lift bag attached to the EM cable appeared.&nbsp; The divers surfaced after a total bottom time of 62 minutes.&nbsp; Eight minutes to spare.&nbsp; We recovered the divers.&nbsp; They reported that the depth of top of the can was at 26 feet (~8m) right where it was supposed to be.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Recovery went smoothly using a single winch equipped with a capstan attachment.&nbsp; By alternately shifting the load from drum (used to lift anchor) and capstan (used to lift instrument we recovered the package and the anchor safely.{color}
{quote}
\\
\\  {color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford.

{color:#cc3300}July 6{color} \-\- Ship by truck D-ESP and supplies for JdF cruise.&nbsp; To Newport, OR.

{color:#cc3300}July 13{color} \-\- Sail for Axial and JdF (1 day late due to weather getting up to Newport)

{color:#cc0000}July 20{color} \-\- recall D-ESP.&nbsp; Recover all instruments.&nbsp; Two more days for Dave Clague.&nbsp; Ship returns July 23.
\\

Aug 17 \-\- Matson picks up loaded ESP van.&nbsp; Genset on truck putting out >530V so our reefer unit will not start.&nbsp; Decide to send due to late hour and ship leaving tomorrow.&nbsp; Van wt. w/ all ESP-Drifter gear: 15,000 lbs.

Sep 9 \-\- Drifting ESP deployed from Kilo Moana N of Station Aloha.&nbsp; Running Bruce w/ MFB ?.

Sep 17 \-\- Drifting ESP recovered.&nbsp; Gear shipped Oct 7 (via DHX and Matson), arrived at MBARI Oct 12..

{color:#9900cc}Nov 2{color} \-\- Install ESP Gordon w/PCR on Santa Cruz Pier.&nbsp; no CTD/ISUS data.&nbsp; Running water quality assay Kevan Yamahara developed. ]]></property>
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# The combination of the phase identifier and the protocol identifier is a "unique key" in determining how much of the various consumables will be used.
# The phases will have worst case times associated with them where they could run up to, but never over, that amount of time.
# The amount of waste storage available and the number of pucks are the main limiting factors.]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.2.jar] to your computer.
# Double-click the jar to run the app.

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|Investigations into Automated Image Analysis].

I'm working on a new method. Documentation is [here|ESP Automated Image Analysis 2]

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter 
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size. 
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[This page lists some terminology and their definitions and context as they were used in the design work of the GUI application.  This is to ensure that when discussions are occurring, we are all talking about the same thing.

# +*Mission*+ This is a logical span of time in which an ESP instrument is operating which has some start and end time.  It is usually associated with a the deployment and recovery of an ESP.
# +*Protocol Run*+ Also just called _protocol_. A sequence of steps (think recipe) that the ESP goes through to achieve a specific goal. Each protocol run will have one puck and filter.
# +*Phase*+ Is a sequence of protocol runs that.  Examples of phases are HAB, BAC, LARV.  The concept of a phase is important as a mission script is defined using phases.
# +*Deployment*+ Is used synonymously with *Mission*.
# +*Mission Script*+ An ASCII file that contains Ruby commands that tell the ESP what actions to take at what times.
# +*Puck*+ Metal ring that holds filter paper which is used to capture and process organisms.
# +*Filter*+ Special paper that is printed with various materials to help in detection of organisms. Not all filters have probes on them (for example, WCR has not probes as it just archives the organisms).
# +*Probe*+
# +*SH*+ Acronym for Sandwich Hybridization
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.3.jar] to your computer.
# Double-click the jar to run the app.

You can also get the automated image analysis application [here|http://www.mbari.org/staff/brian/software/esp-automated-imaging-0.3.jar

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|Investigations into Automated Image Analysis].

I'm working on a new method. Documentation is [here|ESP Automated Image Analysis 2]

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter 
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size. 
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[[|ESPAPP:Betty|Software Revision Level of Betty]
[|ESPAPP:Bruce|Software Revision Level of Bruce]
[|ESPAPP:Moe|Software Revision Level of Moe]
[|ESPAPP:Gordon|Software Revision Level of Gordon]
[|ESPAPP:NEO|Software Revision Level of NEO]
[|ESPAPP:MaCK|Software Revision Level of MaCK]]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
\\
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage taken by Rob Vincent:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]

Map of locations:&nbsp; [http://maps.google.com/maps/ms?ie=UTF&msa=0&msid=213220825771739778963.0004a40bdd601babc291d]

May 23.&nbsp; Attempted recovery of ESP.&nbsp; Message from Roman:

{color:#996600}&nbsp;&nbsp;&nbsp; We went out to the site where espbruce was moored and attempted to find it.&nbsp; The weather was very poor and water was very turbid.&nbsp; Using the ships depth finder we found a promising target.&nbsp; In difficult conditions the divers performed a search but espbruce was not found.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; We recovered the mooring.&nbsp; It looks like the cable was pulled straight out of the cone.&nbsp; The top mast is bent but I cannot say if this was caused by a rough landing on the beach or boat impact.&nbsp; There are no dents or gouges on the mooring.&nbsp; The radio box is dry and antenna looks ok.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; Thursday the RV Gulf Challenger may be able to survey the area with a side scanning sonar.&nbsp; This will be a much better way to search for espbruce.&nbsp;{color}

Message from Roman May 26:

{color:#996600}&nbsp;&nbsp;&nbsp; ESPbruce was located at&nbsp; 43° 02.0740 N&nbsp;&nbsp; 70° 36.8447 W at ~ 10m depth.&nbsp; This position is about 19 yards from the waypoint.&nbsp; So looks like it wasn't dragged and has maintained seal integrity.&nbsp; We will attempt to recover it this weekend if we can get the RV Tioga.&nbsp; If not will recover with the RV Connecticut on june 7th weather permitting.{color}
&nbsp;

Dates for a recovery kept moving as weather and scheduling problems arose.&nbsp; Finally, Roman reported on June 15:
{quote}
{quote}
{color:#996600}ESPbruce was recovered today with no visible external damage. The EM cable strain relief is still on the cable.&nbsp; The recovery operation used two ships the RV Gulf Challenger and it's sister the RV Tioga.&nbsp; The Challenger supported the the side scan survey and the Tioga supported the divers and lifting of the core package and its anchor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;The side scan sonar operator advised me at the beginning of the day that he believed the esp package would be found on the bottom.&nbsp; He based this opinion on the data secured by his colleague almost two weeks ago.&nbsp; From his read of that run, he believed that the instrument was 15m off the bottom at that time.&nbsp; Depth at this site is 49m.&nbsp; He felt that the instrument was slowly sinking and that by today it was surly be on the sea floor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Todays side scan survey took approximately 90 minutes.&nbsp; They had acquired a strong signature on the core and calculated that it was at a depth of 65 feet (~20m). The package&nbsp; was still located within 10m of the original deployment site.&nbsp; They dropped a marker line with a float as close to the calculated position as possible.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;At this point divers equipped with twin 80 cu ft Nitrox cylinders and electric scooters dived on the marker.&nbsp; They had 70 minutes of search time.&nbsp; After 42 minutes an orange sausage float attached to a spectra lift line appeared.&nbsp; Then 10 minutes later a second lift bag attached to the EM cable appeared.&nbsp; The divers surfaced after a total bottom time of 62 minutes.&nbsp; Eight minutes to spare.&nbsp; We recovered the divers.&nbsp; They reported that the depth of top of the can was at 26 feet (~8m) right where it was supposed to be.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Recovery went smoothly using a single winch equipped with a capstan attachment.&nbsp; By alternately shifting the load from drum (used to lift anchor) and capstan (used to lift instrument we recovered the package and the anchor safely.{color}
{quote}
\\
\\  {color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford.

{color:#cc3300}July 6{color} \-\- Ship by truck D-ESP and supplies for JdF cruise.&nbsp; To Newport, OR.

{color:#cc3300}July 13{color} \-\- Sail for Axial and JdF (1 day late due to weather getting up to Newport)

{color:#cc0000}July 20{color} \-\- recall D-ESP.&nbsp; Recover all instruments.&nbsp; Two more days for Dave Clague.&nbsp; Ship returns July 23.
\\

Aug 17 \-\- Matson picks up loaded ESP van.&nbsp; Genset on truck putting out >530V so our reefer unit will not start.&nbsp; Decide to send due to late hour and ship leaving tomorrow.&nbsp; Van wt. w/ all ESP-Drifter gear: 15,000 lbs.

Sep 9 \-\- Drifting ESP deployed from Kilo Moana N of Station Aloha.&nbsp; Running Bruce w/ MFB ?.

Sep 17 \-\- Drifting ESP recovered.&nbsp; Gear shipped Oct 7 (via DHX and Matson), arrived at MBARI Oct 12.. ]]></property>
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<property name="body"><![CDATA[Present: Cheri,  Doug, Brent, Jim

Absent:&nbsp; Chris S., Scott

h3. Machine Builds

* Scott provided rough board prices.&nbsp; Numbers and invoice sent to Mike Pinto to bill McLane.&nbsp; Money to be returned to 900915.
* Most recent drawings for screens are here--> [SH1 screen|^SH1 Frit drawing revB.pdf|SH1 screen drawing] and [WCR screen|^WCR dispersion Screen drawing revA.pdf|WCR screen drawing].
* Screen drawings have been modified so holes are smaller (=stiffer metal).&nbsp; Must compare to PO drawings to find most recent.
* Cheri tasked with assembling a 'spare' kit and we will get this&nbsp; x3

h3. MFB&nbsp;


h3. Drifter


h3. Software


h3. Deep ESP/DWSM

* Over weekend, water was inadvertently let into the sphere (~500ml) due to the wrong puck (LAF) being loaded.&nbsp; All things looked okay, until we tried the next SH1, and the puck heater started giving wild readings.&nbsp; It is probably fried.&nbsp; We will run some core negative PCRs, and recover next week (Tuesday) if weather permits.

h3. GUI


h3. Deployment Issues

* Brent working on networking the pier deployment.&nbsp; Will acquire larger antenna(s) and working on VPN issues.&nbsp; Possible trip down there Weds.&nbsp; Deployment looking to be during the week of the 19th.
* Doug will talk to science about designing the Pier-water Introduction System (PIS).

h3. &nbsp;Other Items

* Harbans Dhadwal (Stoney Brook, NY) will be&nbsp; visiting Friday, Oct 30.&nbsp; He'll be learning about basic MFB functions.&nbsp; Will need a 'cheat sheet' of commands, and maybe the 'training' can used colored water.&nbsp; Cheri on this.]]></property>
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<property name="body"><![CDATA[Present: Cheri,  Doug, Brent, Jim

Absent:&nbsp; Chris S., Scott

h3. Machine Builds

* Scott provided rough [board prices|^McLane Cost Estimate.xls|Core Board Costs].&nbsp; Numbers and invoice sent to Mike Pinto to bill McLane.&nbsp; Money to be returned to 900915.
* Most recent drawings for screens are here--> [SH1 screen|^SH1 Frit drawing revB.pdf|SH1 screen drawing] and [WCR screen|^WCR dispersion Screen drawing revA.pdf|WCR screen drawing].
* Screen drawings have been modified so holes are smaller (=stiffer metal).&nbsp; Must compare to PO drawings to find most recent.
* Cheri tasked with assembling a 'spare' kit and we will get this&nbsp; x3

h3. MFB&nbsp;


h3. Drifter


h3. Software


h3. Deep ESP/DWSM

* Over weekend, water was inadvertently let into the sphere (~500ml) due to the wrong puck (LAF) being loaded.&nbsp; All things looked okay, until we tried the next SH1, and the puck heater started giving wild readings.&nbsp; It is probably fried.&nbsp; We will run some core negative PCRs, and recover next week (Tuesday) if weather permits.

h3. GUI


h3. Deployment Issues

* Brent working on networking the pier deployment.&nbsp; Will acquire larger antenna(s) and working on VPN issues.&nbsp; Possible trip down there Weds.&nbsp; Deployment looking to be during the week of the 19th.
* Doug will talk to science about designing the Pier-water Introduction System (PIS).

h3. &nbsp;Other Items

* Harbans Dhadwal (Stoney Brook, NY) will be&nbsp; visiting Friday, Oct 30.&nbsp; He'll be learning about basic MFB functions.&nbsp; Will need a 'cheat sheet' of commands, and maybe the 'training' can used colored water.&nbsp; Cheri on this.]]></property>
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<property name="body"><![CDATA[Present: Cheri,  Doug, Brent, Jim

Absent:&nbsp; Chris S., Scott


h3. Machine Builds

* Scott provided rough board prices.&nbsp; Numbers and invoice sent to Mike Pinto to bill McLane.&nbsp; Money to be returned to 900915.
* Most recent drawings for screens are [here|screen drawings].
* Screen drawings have been modified so holes are smaller (=stiffer metal).&nbsp; Must compare to PO drawings to find most recent.
* Cheri tasked with assembling a 'spare' kit and we will get this&nbsp; x3

h3. MFB&nbsp;


h3. Drifter


h3. Software


h3. Deep ESP/DWSM

* Over weekend, water was inadvertently let into the sphere (~500ml) due to the wrong puck (LAF) being loaded.&nbsp; All things looked okay, until we tried the next SH1, and the puck heater started giving wild readings.&nbsp; It is probably fried.&nbsp; We will run some core negative PCRs, and recover next week (Tuesday) if weather permits.

h3. GUI


h3. Deployment Issues

* Brent working on networking the pier deployment.&nbsp; Will acquire larger antenna(s) and working on VPN issues.&nbsp; Possible trip down there Weds.&nbsp; Deployment looking to be during the week of the 19th.
* Doug will talk to science about designing the Pier-water Introduction System (PIS).

h3. &nbsp;Other Items

* Harbans Dhadwal (Stoney Brook, NY) will be&nbsp; visiting Friday, Oct 30.&nbsp; He'll be learning about basic MFB functions.&nbsp; Will need a 'cheat sheet' of commands, and maybe the 'training' can used colored water.&nbsp; Cheri on this.]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision
# [25Jun2009]
# 02Jul2009 - no meeting; 4th of July break
# [09Jul2009]
# [16Jul2009]
# [23Jul2009]
# 30Jul2009 - Scott ran mtg; proposal preparation
# [06Aug2009]
# 13Aug2009 - cancelled; proposal/grant preparations
# [20Aug2009]
# 27Aug2009 - Jim Vacation; Scott in charge
# 03Sep2009 - Jim Vacation; Scott in charge
# [10Sep2009]
# [01Oct2009]
# [08Oct2009]]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]]]></property>
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<property name="body"><![CDATA[# [2008 Q1-Q2 Schedule (rev 1)]
# [2008 Q1-Q2 Schedule (rev 2)]
# [2008 Q1-Q2 Schedule (rev 3)]
# [2008 Q1-Q2 Schedule (rev 4)]
# [2008 Q1-Q2 Schedule (rev 5)]
# [Machinist build schedule (Feb 2008)]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}

h4. Administrative Items

{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}


{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h2. Lessons Learned meeting after Drifter Cruise

* Shipping van fan velocity needs to be turned down if we are to work inside.  Noise is not too bad, but air velocity stirs up lots of dust.
* Van left MBARI Aug 17, arrived Hawaii Aug 25.  KM deployed Sep 6.  This was barely enough time to get everything ready.  In future, when running PCR, we need {color:#ff0000}3 weeks minimum{color} to prepare.
* MFB preparations.  We should get it ready, but once arrived, do full runs and spot-compare to pre-shipping.
* Must have extra tools here at home, so traveling group does not clean us out.
* Rigging box spares in case we deploy back home at same time.
* This deployment (Sep 7-17) used 1400 minutes of Iridium air time.  Was slow and dropped frequently.  Seas were calm so no need for constant engineering data to be transferred.
** Was discussion of how to compress files to more efficiently send via Iridium.  Perhaps .JPG conversion of TIFF's?
* Retrieved NO DATA from the PAR sensor.  PAR log says it rec'd a ctrl-C character, which stopped data logging.  Perhaps happened when ESP re-powered?  We need either NO comms to PAR so it's always running, or TOTAL comms, so we can query it and restart if necessary.
* Important to time-sync all ADCP's with the ship.

Many other engineering issues learned are in this document:
# [Lessons Learned from CMORE Hawaii cruise (Sept 2011)|^Lessons Learned.docx|Lessons Learned]]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision
# [25Jun2009]
# 02Jul2009 - no meeting; 4th of July break
# [09Jul2009]
# [16Jul2009]
# [23Jul2009]
# 30Jul2009 - Scott ran mtg; proposal preparation
# [06Aug2009]
# 13Aug2009 - cancelled; proposal/grant preparations
# [20Aug2009]
# 27Aug2009 - Jim Vacation; Scott in charge
# 03Sep2009 - Jim Vacation; Scott in charge
# [10Sep2009]
# [01Oct2009]
# [08Oct2009]
# [15Oct2009]]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Birch, Everlove, Jensen, Pargett, Gomes, Scholin

h3. Mack Deployment begins April 3

\\

Mack out of cold, and getting new lid.
Science still to drain waste and add new flush

Will perform 2 runs tomorrow (Friday).&nbsp; A pre-can DA (short) to confirm reagents work, then a full DA.

Monday will load pucks and can it.
Tuesday mount to mooring.
\\

Divers \-\- Mike Conway, Jason Felton

Crew \-\- Roman, Scott, Doug, Cheri, Jim

Discussion ensued about our can situation.&nbsp; We have two cans (a good one, and a stitch-welded one) and there was talk on logistics for this 2.5 month network deployment.&nbsp;

Current schedule is

&nbsp;Deployment 1 is April 3-21 (Mack delivered on Shanna Rae, retrieved by Zephyr).&nbsp;
&nbsp;Deployment 2 is May1-27 (Mack delivered and retrieved by Zephyr).
&nbsp;Deployment 3 will be 2 ESPs (M0 and off SC) May 28-June 30 (Neo and a refitted Bruce via Zephyr)
&nbsp;]]></property>
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<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically (colors are same deployment)+

{color:#ff00ff}April 6--Bruce at M0 for surface deployment (Zephyr){color}

April 15--Mack in Sphere (dive #1) for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in Sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

{color:#ff00ff}April 29--Recover Bruce at M0 (Zephyr){color}

May 1--Mack in Sphere (dive #3) connected to DWSM; incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

{color:#0033cc}May 14--Deploy NEO w/PCR, surface deployment (Zephyr){color}

May 27--First Drifter dive; used weighted cable (Zephyr)

June 5-9 \-\- Western Flyer Trip.&nbsp; D-ESP, Drifter, and CTD casts. {color:#cc0000}{*}MOVIES{*}{color}:  D-ESP launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/DESP%20deployment%20(full%20quality).dv].  Drifter launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/Drifter.dv].

{color:#0033cc}June 11 \-\- Recover NEO.&nbsp; (Zephyr){color}\\

+FALL Network Deployment+

Proposed locations are here: [http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&msid=113879459163411006053.000471828af997bd7d89c&t=h&z=12]

September 24 \-\- Deploy Moe w/PCR at M0.&nbsp; Deployed Mack at Santa Cruz.&nbsp; {color:#66cc00}Deployed Bruce in the bight.&nbsp; (Zephyr)&nbsp; Lost communications with Bruce that day.{color}

{color:#66cc00}September 28 \-\- Recover (dead) Bruce.&nbsp; Comms box had water in it, but radio worked.&nbsp; EM cable had 2 broken wires. (Zephyr){color}

September 30 \-\- Deploy D-ESP on MARS (Lobos).&nbsp; Hand issue at first, but 'fixed' itself.&nbsp; Worked until Oct. 7 when wrong puck was loaded and water introduced into core, frying puck heater.&nbsp; We turned off and first recovery day (Oct 13) is weathered out.&nbsp; It still awaits recovery.

{color:#66cc00}October 14 \-\- Re-deploy Bruce (Zephyr).&nbsp; New comms box, re-terminated EM cable.&nbsp; Working well after deployment.{color}]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15-18, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;

*Jun 6, 2017*

Rich Walsh of SCRIPPS went to buoy and swapped the non-working MELO with a newer one that we had sent down.&nbsp; We are now getting hourly (correct) positions.

*Sept 6, 2017*

Final recovery of Waldo.

h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 27\- May 8, 2017*

This was part of a 5-vehicle launch (Tethys, Daphne, Aku w/ ESP Honu, Ahi, Opah).&nbsp; Gabe Foreman arrived from UH to help with piloting.&nbsp; Adam Jones helped launch Aku and Opah.

Ran multiple simulation to test the mission.

On Weds, May 3, tried first 'real' concurrent sampling.&nbsp; Cartridge 1 threw an alignment error--could not push on plunge valve.&nbsp; We labeled that cartridge 'wet' and moved to cartridge 2.&nbsp; But this notification not written to file, and was lost when power was cycled.&nbsp; Thus, we thought we were onto cartridge #2, but in reality were on #1 (which started working....).&nbsp; Sampling was as follows:

&nbsp;All cartridges started filtering at 60m depth while vehicle ascended to surface, where filtering stopped.&nbsp; WF took CTD casts in the same area at same time.&nbsp; Kevan took 2L each from each of these bottles: 60m, 40m, 20m, 10m, surface and mixed the 10L in a carboy.&nbsp; From that carboy, he sampled 1L through a cartridge on tackle-box, and 1L (x3) on peristaltic.&nbsp; Sample #2 had 1L (x3) through the tacklebox cartridge.&nbsp; Francisco took 1L from each of those depths and peristaltic filtered.

&nbsp;Because of the cartridge number mix-up, Honu returned with a dry #5 cartridge, which we ran as a negative control in the lab.&nbsp; Investigation of the alignment issues is ongoing.
\\

h3. Summary of 3G flights to this point (May 2017):

{panel}
*Nov* {color:#0000ff}2014{color} &nbsp;
Very first 3G flight.&nbsp; Makai with one Archive cartridge.&nbsp; Mission lasted \~3 days.
\_____________________\_
*July* {color:#0000ff}2015{color} &nbsp;
First 5-cartridge flight on Makai.&nbsp; All Archive.&nbsp; Cartridge 1 toroid valve stuck in bypass mode, thus recovered only 4 sample filters.&nbsp; All collected <20m deep.

*Dec* {color:#0000ff}2015{color} &nbsp;
First 4 & 1 (archive/LnG) flight on Makai.&nbsp; Many vehicle errors.&nbsp; No stratification so difficult to find any 'features'.&nbsp; Acquired 2 archives and 1 LnG.&nbsp; rough weather recovery.&nbsp; I don't have actual collection depths for these three samples.
\_____________________\_
*Feb* {color:#0000ff}2016{color} &nbsp;
Repeat Dec flight.&nbsp; 1 LnG fired first, then 4 Archives on Makai.&nbsp; Samples taken at 8.7m, 12.7m, 13m, 27m, and 27m.

*Dec* {color:#0000ff}2016{color} &nbsp;
Depth testing with Honu in Makai.&nbsp; 5 archival cartridges.&nbsp; Fired at chl max (~14m), 50m, and 100m.&nbsp; 200m cartridge started, but vehicle cut ESP power before finished.&nbsp; 300m sample had carousel alignment issue and did not complete.&nbsp; 3 of 5 samples preserved.
\_____________________\_
*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; meet with R/V Shimada (CALCOFI ship).&nbsp; Difficulties with water in payload section and rough recovery.&nbsp; Three filters recovered (chl-max to compare to Shimada's, and two at 10m)

*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; CANON cruise and WF rendezvous.&nbsp; Alignment problem had us bypass (so we thought) cartridge #1.&nbsp; Four archives collected, two a smear from 40m to surface, two from 60m to surface.&nbsp; These are matched to ship samples Kevan collected.
\_____________________\_

Overall, we have 21 archival filters that correctly filtered and preserved samples; two LnG samples were collected (were both run through SPR on the vehicle?)
{panel}

h4. {color:#ff00cc}Makai flight w ESP-Koa and 60 Archive Cartridges{color}

*Dec 12 - 19, 2017*

We decided to generate 5 'blocks' of behavior (below) each testing a certain collection scheme, with replicates.&nbsp; Combined samples for Ed with samples for eDNA work.

Out of 60 cartridges, 15 are controls (9 pre-experiment + 6 post-experiment); 45 will be fired offshore.
The 45 field samples are divided into 5 blocks, each block containing 9 samples.
In each 9-sample block, firings are in triplicate bursts: 1, 2, 3 in one continuous burst; then 4, 5, 6; and then 7, 8, 9.

Scientists and engineers will jointly select appropriate sampling locations in consideration of oceanographic features as well as LRAUV operation safety.

Block 1 (Bathymetry alert due to deep sampling):
Mission files:
chlpeak_sampling_InAboveBelow.xml, in donut mode.
depth_sequence_sampling.xml
First, vehicle transits to M1-northeast: 36.760, \-122.012
Then, kick off mission, setting waypoint to M1. Vehicle will do an horizontal search for high chl between M1-northeast \[36.760, \-122.012\] and M1 \[36.750, \-122.022\]; set the hi-chl spot as the sampling location; run a cylinder around the sampling location
Run chlpeak_sampling_InAboveBelow.xml:
3 samples at vertical chl peak depth
Then, run depth_sequence_sampling.xml:
3 samples at 100m depth
3 samples at 250m depth
Total: 9 samples, \~15 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time).

Block 2 (Bathymetry alert due to deep sampling):
Mission file: smear_sampling.xml, in donut mode, on the first 3 samples.
Mission file: depth_sequence_sampling.xml, in donut mode, on the remaining 6 samples.
3 samples smearing between 5m and 100m depths
3 samples at 100m depth
3 samples at 5m depth
Total: 9 samples, \~14 hours (presuming 1hr filtration time + 0.5hr processing time for each sample)

Block 3:
Mission file: isotherm_sampling.xml, in donut mode.
Initial horizontal search for high chl in local area; set the hi-chl spot as the sampling location; run a cylinder around sampling location
3 samples at the temperature corresponding to the vertical chl peak.
3 samples at chlpeak temp - deltaT1
3 samples at chlpeak temp + deltaT2
Total: 9 samples, \~15 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time).

Block 4:
Mission file: chlpeak_sampling_InAboveBelow.xml.xml, in drift mode.
Initial horizontal search for high chl in local area; set the hi-chl spot as the sampling location; run a cylinder around sampling location
3 samples at chl peak depth
Vertical perturbation to reacquire chl peak
3 samples at chl peak depth
Vertical perturbation to reacquire chl peak
3 samples at chl peak depth
Total: 9 samples, \~16 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time + vertical perturbation time).

Block 5:
Mission file: depth_sequence_sampling.xml, in donut mode
Scientists determine a horizontal feature, and set a certain depth for sampling
3 samples at the set depth on one side of feature
3 samples at same depth in feature
3 samples at same depth on other side of feature
Total: 9 samples, \~16 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + transit time)]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes (no longer maintained--Sep 2012)

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments](MB)
# [2009 Deployments](MB, MARS, SC Wharf)
# [2010 Deployments] (MB, SoCAL, Methane Mound, Drifter, MARS, SC Pier)
# [2011 Deployments](MB, GoM, Axial, Drifter-HI, SC Pier)
# [2012 Deployments] (MB, New Zealand, SoCAL, Friday Harbor, GoM, Drifter)
# [2013 Deployments] (MB, SoCAL, MARS, Puget Sound)
# [2014 Deployments] (MB, San Diego, Catalina, SoCAL, 3G)
# [2015 Deployments] (MB, SCRIPPS, 3G)
# [2016 Deployments] (3G in MB twice, SCRIPPS, Moran)
# [2017 Deployments] (3G, SCRIPPS...)
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[{color:#ff0099}Our current (July, 2014) puck count is{color} {color:#ff0099}[{color:#ff0099}here{color}|^2014_PUCK _INVENTORYv2.xlsx|MBARI puck count]{color}{color:#ff0099}.{color}\\

Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note that we have yet to make a full batch of high-volume snap pucks, but when we do, those will be labeled 1HV (top and bottom).

Here is who is doing our etching:

LaserMark
2109 O'Toole Ave. Ste S
San Jose, CA 95131
Phone 408 433-9333
Fax 408 433-9343
\\
\\

Here is what I have packed up for etching:
| Type | Top/bottom | Numbered | Amount | NOTE |
| WCR | Top | 040-079 | 40 | \\ |
| \\ | Bottom | 040-079 | 40 | \\ |
| LAF | Top | 040-078 | 39 | 1=Missing |
| \\ | Bottom | 040-078 | 39 | 1=Missing |
| SAF | Top | 040-075 | 36 | 4sent to Gregg D |
| \\ | Bottom | 040-075 | 36 | 4sent to Gregg D |
| SHT | Top | 080-159 | 80 | \\ |
| SH1 | Bottom | 080-159 | 80 | \\ |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 390 | \\ |
\\
\\

I also sent 1 WCR puck (top&bottom) as a font sample.&nbsp; When these come back I will pack up the ones that are to be re-numbered(SHT2000-079).&nbsp; I haven't received a quote yet but Laser Mark said about $2 each piece + shipping.
\\

{color:#ff0000}UPDATE 3/24/08{color}

The SH1 tops that were misprinted are going to be sent out tomorrow to be re etched along with one of the LAF's that escaped detection last time:
| Type | Top/bottom | Numbered | Amount | NOTE |
| LAF | Top | 079 | 1 | Found the Lost 1\! |
| \\ | Bottom | 079 | 1 | \\ |
| SHT | Top | 000-079 | 80 | Old etching to be X'd out |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 82 | \\ |
That is all for now
\\
\\
\\

{color:#ff0000}UPDATE 2/24/09&nbsp; There have been several iterations of the above serialization process since this was last updated.{color}&nbsp;

Here is where we now stand:
| This   is an inventory of pucks that have been serialized and are available for   use.&nbsp; | \\ | \\ | \\ |
| There are   aprox. 1200 more pieces (or 600 more pucks) that have yet to be serialized. | \\ | \\ |
| They are   located in the 'B' building lab | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| Type | Top/Bottom | Lot 2 | Lot 2 | Lot 3 | Lot 3 | Lot 4 | Total | \\ |
| WCR | Top | 40 | 40 | 40 | 39 | 40 | 199 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 40 | 40 | 200 | \\ |
| LAF | Top | 40 | 40 | 40 | 38 | 40 | 198 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 36 | 40 | 196 | \\ |
| SAF | Top | 40 | 36 | 40 | 39 | 40 | 195 | \\ |
| \\ | Bottom | 40 | 36 | 40 | 40 | 40 | 196 | \\ |
| SHT | Top | 80 | 80 | 80 | 80 | 80 | 400 | \\ |
| SH1 \\ | Bottom | 80 | 80 | 80 | 77 | 80 | 397 | \\ |
| Total | \\ | 400 | 392 | 400 | 389 | 400 | 1981 | 990.5 |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | pieces | pucks |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| The   lot number refers to the 4th place in the serialization code:&nbsp; | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 letter type | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 1 digit lot number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 digit individual part number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| All parts   are numbered 000-079 ( except where some are missing) for each lot EXCEPT for : | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SHT=000-159 | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SH1=000-159 | \\ | \\ | \\ | \\ |
{color:#ff0000}{*}UPDATE August 11, 2010{*}{color}

&nbsp;Puck order from McLane arrived.

Rec'd&nbsp; 160 SH1, and 80 ea of LAF, SAF, WCR, HV (consists of HV top and SH1 bottom), all laser-etched.

PO 1010318
\\

Here is their email explaining their numbering system (sent Jan 14, 2010):
{Info:title=Mclane Numbering Scheme}
{Info}
From: Tim Shanahan \[mailto:tshanahan@mclanelabs.com\]
Sent: Thursday, January 14, 2010 8:52 AM
To: 'Birch, James'
Cc: 'Pargett, Douglas'; 'Jensen, Scott'; Everlove, Cheri; 'Scholin, Chris';
Yuki Honjo (yhonjo@mclanelabs.com); Ivory Engstrom
(iengstrom@mclanelabs.com); Mike Mathewson (mathewson@mclanelabs.com)
Subject: Puck serial number format

Hello All,

We've been thinking about the serial number format for the pucks and we'd
like to suggest some modifications.&nbsp; I'm concerned about duplicating lot
numbers and the potential for having runs bigger than 1000 units.

At least for now, I think there's the possibility of McLane and MBARI still
continuing to make puck independently.&nbsp; Keeping track of the current lot
number could be problematic.

So I propose the following:

TTTMYYSSSS

TTT for type code as below.

MYY for date code in
M= 1 - 9 for Jan - Sept, A B or C for Oct Nov & Dec

YY for 2 digit year

SSSS for serial number 0000 - 9999

Also, this ensures that there never a letter I or O.

This increases the total number of characters from 7 to 10.
{info}
{info}
&nbsp;
\\
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15-18, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;

*Jun 6, 2017*

Rich Walsh of SCRIPPS went to buoy and swapped the non-working MELO with a newer one that we had sent down.&nbsp; We are now getting hourly (correct) positions.

*Sept 6, 2017*

Final recovery of Waldo.

h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 27\- May 8, 2017*

This was part of a 5-vehicle launch (Tethys, Daphne, Aku w/ ESP Honu, Ahi, Opah).&nbsp; Gabe Foreman arrived from UH to help with piloting.&nbsp; Adam Jones helped launch Aku and Opah.

Ran multiple simulation to test the mission.

On Weds, May 3, tried first 'real' concurrent sampling.&nbsp; Cartridge 1 threw an alignment error--could not push on plunge valve.&nbsp; We labeled that cartridge 'wet' and moved to cartridge 2.&nbsp; But this notification not written to file, and was lost when power was cycled.&nbsp; Thus, we thought we were onto cartridge #2, but in reality were on #1 (which started working....).&nbsp; Sampling was as follows:

&nbsp;All cartridges started filtering at 60m depth while vehicle ascended to surface, where filtering stopped.&nbsp; WF took CTD casts in the same area at same time.&nbsp; Kevan took 2L each from each of these bottles: 60m, 40m, 20m, 10m, surface and mixed the 10L in a carboy.&nbsp; From that carboy, he sampled 1L through a cartridge on tackle-box, and 1L (x3) on peristaltic.&nbsp; Sample #2 had 1L (x3) through the tacklebox cartridge.&nbsp; Francisco took 1L from each of those depths and peristaltic filtered.

&nbsp;Because of the cartridge number mix-up, Honu returned with a dry #5 cartridge, which we ran as a negative control in the lab.&nbsp; Investigation of the alignment issues is ongoing.
\\

h3. Summary of 3G flights to this point (May 2017):

{panel}
*Nov* {color:#0000ff}2014{color} &nbsp;
Very first 3G flight.&nbsp; Makai with one Archive cartridge.&nbsp; Mission lasted \~3 days.
\_____________________\_
*July* {color:#0000ff}2015{color} &nbsp;
First 5-cartridge flight on Makai.&nbsp; All Archive.&nbsp; Cartridge 1 toroid valve stuck in bypass mode, thus recovered only 4 sample filters.&nbsp; All collected <20m deep.

*Dec* {color:#0000ff}2015{color} &nbsp;
First 4 & 1 (archive/LnG) flight on Makai.&nbsp; Many vehicle errors.&nbsp; No stratification so difficult to find any 'features'.&nbsp; Acquired 2 archives and 1 LnG.&nbsp; rough weather recovery.&nbsp; I don't have actual collection depths for these three samples.
\_____________________\_
*Feb* {color:#0000ff}2016{color} &nbsp;
Repeat Dec flight.&nbsp; 1 LnG fired first, then 4 Archives on Makai.&nbsp; Samples taken at 8.7m, 12.7m, 13m, 27m, and 27m.

*Dec* {color:#0000ff}2016{color} &nbsp;
Depth testing with Honu in Makai.&nbsp; 5 archival cartridges.&nbsp; Fired at chl max (~14m), 50m, and 100m.&nbsp; 200m cartridge started, but vehicle cut ESP power before finished.&nbsp; 300m sample had carousel alignment issue and did not complete.&nbsp; 3 of 5 samples preserved.
\_____________________\_
*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; meet with R/V Shimada (CALCOFI ship).&nbsp; Difficulties with water in payload section and rough recovery.&nbsp; Three filters recovered (chl-max to compare to Shimada's, and two at 10m)

*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; CANON cruise and WF rendezvous.&nbsp; Alignment problem had us bypass (so we thought) cartridge #1.&nbsp; Four archives collected, two a smear from 40m to surface, two from 60m to surface.&nbsp; These are matched to ship samples Kevan collected.
\_____________________\_

Overall, we have 21 archival filters that correctly filtered and preserved samples; two LnG samples were collected (were both run through SPR on the vehicle?)
{panel}

h4. {color:#ff00cc}Makai flight w ESP-Koa and 60 Archive Cartridges{color}

*Dec 12 - 19, 2017*

We decided to generate 5 'blocks' of behavior (below) each testing a certain collection scheme, with replicates.&nbsp; Combined samples for Ed with samples for eDNA work.

Out of 60 cartridges, 15 are controls (9 pre-experiment + 6 post-experiment); 45 will be fired offshore.
The 45 field samples are divided into 5 blocks, each block containing 9 samples.
In each 9-sample block, firings are in triplicate bursts: 1, 2, 3 in one continuous burst; then 4, 5, 6; and then 7, 8, 9.

Scientists and engineers will jointly select appropriate sampling locations in consideration of oceanographic features as well as LRAUV operation safety.

Block 1 (Bathymetry alert due to deep sampling):
Mission files:
chlpeak_sampling_InAboveBelow.xml, in donut mode.
depth_sequence_sampling.xml
First, vehicle transits to M1-northeast: 36.760, \-122.012
Then, kick off mission, setting waypoint to M1. Vehicle will do an horizontal search for high chl between M1-northeast \[36.760, \-122.012\] and M1 \[36.750, \-122.022\]; set the hi-chl spot as the sampling location; run a cylinder around the sampling location
Run chlpeak_sampling_InAboveBelow.xml:
3 samples at vertical chl peak depth
Then, run depth_sequence_sampling.xml:
3 samples at 100m depth
3 samples at 250m depth
Total: 9 samples, \~15 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time).

Block 2 (Bathymetry alert due to deep sampling):
Mission file: smear_sampling.xml, in donut mode, on the first 3 samples.
Mission file: depth_sequence_sampling.xml, in donut mode, on the remaining 6 samples.
3 samples smearing between 5m and 100m depths
3 samples at 100m depth
3 samples at 5m depth
Total: 9 samples, \~14 hours (presuming 1hr filtration time + 0.5hr processing time for each sample)

Block 3:
Mission file: isotherm_sampling.xml, in donut mode.
Initial horizontal search for high chl in local area; set the hi-chl spot as the sampling location; run a cylinder around sampling location
3 samples at the temperature corresponding to the vertical chl peak.
3 samples at chlpeak temp - deltaT1
3 samples at chlpeak temp + deltaT2
Total: 9 samples, \~15 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time).

Block 4:
Mission file: chlpeak_sampling_InAboveBelow.xml.xml, in drift mode.
Initial horizontal search for high chl in local area; set the hi-chl spot as the sampling location; run a cylinder around sampling location
3 samples at chl peak depth
Vertical perturbation to reacquire chl peak
3 samples at chl peak depth
Vertical perturbation to reacquire chl peak
3 samples at chl peak depth
Total: 9 samples, \~16 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time + vertical perturbation time).

Block 5:
Mission file: depth_sequence_sampling.xml, in donut mode
Scientists determine a horizontal feature, and set a certain depth for sampling
3 samples at the set depth on one side of feature
3 samples at same depth in feature
3 samples at same depth on other side of feature
Total: 9 samples, \~16 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + transit time)

Vehicle recovered Dec 19, and discovered pulled wire on toroid valve.&nbsp; Toroid pins never moved, so each sampling event pumped through ring (thus the constancy in filtering times).&nbsp; All filters were preserved with RNALater, but none had any biomass.&nbsp; Severe disappointment.&nbsp; Next flight will be late January 2018.]]></property>
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<property name="body"><![CDATA[Our current (July, 2014) puck count is [here|^2014_PUCK _INVENTORYv2.xlsx|MBARI puck count].
\\

Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note that we have yet to make a full batch of high-volume snap pucks, but when we do, those will be labeled 1HV (top and bottom).

Here is who is doing our etching:

LaserMark
2109 O'Toole Ave. Ste S
San Jose, CA 95131
Phone 408 433-9333
Fax 408 433-9343
\\
\\

Here is what I have packed up for etching:
| Type | Top/bottom | Numbered | Amount | NOTE |
| WCR | Top | 040-079 | 40 | \\ |
| \\ | Bottom | 040-079 | 40 | \\ |
| LAF | Top | 040-078 | 39 | 1=Missing |
| \\ | Bottom | 040-078 | 39 | 1=Missing |
| SAF | Top | 040-075 | 36 | 4sent to Gregg D |
| \\ | Bottom | 040-075 | 36 | 4sent to Gregg D |
| SHT | Top | 080-159 | 80 | \\ |
| SH1 | Bottom | 080-159 | 80 | \\ |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 390 | \\ |
\\
\\

I also sent 1 WCR puck (top&bottom) as a font sample.&nbsp; When these come back I will pack up the ones that are to be re-numbered(SHT2000-079).&nbsp; I haven't received a quote yet but Laser Mark said about $2 each piece + shipping.
\\

{color:#ff0000}UPDATE 3/24/08{color}

The SH1 tops that were misprinted are going to be sent out tomorrow to be re etched along with one of the LAF's that escaped detection last time:
| Type | Top/bottom | Numbered | Amount | NOTE |
| LAF | Top | 079 | 1 | Found the Lost 1\! |
| \\ | Bottom | 079 | 1 | \\ |
| SHT | Top | 000-079 | 80 | Old etching to be X'd out |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 82 | \\ |
That is all for now
\\
\\
\\

{color:#ff0000}UPDATE 2/24/09&nbsp; There have been several iterations of the above serialization process since this was last updated.{color}&nbsp;

Here is where we now stand:
| This   is an inventory of pucks that have been serialized and are available for   use.&nbsp; | \\ | \\ | \\ |
| There are   aprox. 1200 more pieces (or 600 more pucks) that have yet to be serialized. | \\ | \\ |
| They are   located in the 'B' building lab | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| Type | Top/Bottom | Lot 2 | Lot 2 | Lot 3 | Lot 3 | Lot 4 | Total | \\ |
| WCR | Top | 40 | 40 | 40 | 39 | 40 | 199 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 40 | 40 | 200 | \\ |
| LAF | Top | 40 | 40 | 40 | 38 | 40 | 198 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 36 | 40 | 196 | \\ |
| SAF | Top | 40 | 36 | 40 | 39 | 40 | 195 | \\ |
| \\ | Bottom | 40 | 36 | 40 | 40 | 40 | 196 | \\ |
| SHT | Top | 80 | 80 | 80 | 80 | 80 | 400 | \\ |
| SH1 \\ | Bottom | 80 | 80 | 80 | 77 | 80 | 397 | \\ |
| Total | \\ | 400 | 392 | 400 | 389 | 400 | 1981 | 990.5 |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | pieces | pucks |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| The   lot number refers to the 4th place in the serialization code:&nbsp; | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 letter type | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 1 digit lot number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 digit individual part number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| All parts   are numbered 000-079 ( except where some are missing) for each lot EXCEPT for : | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SHT=000-159 | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SH1=000-159 | \\ | \\ | \\ | \\ |
{color:#ff0000}{*}UPDATE August 11, 2010{*}{color}

&nbsp;Puck order from McLane arrived.

Rec'd&nbsp; 160 SH1, and 80 ea of LAF, SAF, WCR, HV (consists of HV top and SH1 bottom), all laser-etched.

PO 1010318
\\

Here is their email explaining their numbering system (sent Jan 14, 2010):
{Info:title=Mclane Numbering Scheme}
{Info}
From: Tim Shanahan \[mailto:tshanahan@mclanelabs.com\]
Sent: Thursday, January 14, 2010 8:52 AM
To: 'Birch, James'
Cc: 'Pargett, Douglas'; 'Jensen, Scott'; Everlove, Cheri; 'Scholin, Chris';
Yuki Honjo (yhonjo@mclanelabs.com); Ivory Engstrom
(iengstrom@mclanelabs.com); Mike Mathewson (mathewson@mclanelabs.com)
Subject: Puck serial number format

Hello All,

We've been thinking about the serial number format for the pucks and we'd
like to suggest some modifications.&nbsp; I'm concerned about duplicating lot
numbers and the potential for having runs bigger than 1000 units.

At least for now, I think there's the possibility of McLane and MBARI still
continuing to make puck independently.&nbsp; Keeping track of the current lot
number could be problematic.

So I propose the following:

TTTMYYSSSS

TTT for type code as below.

MYY for date code in
M= 1 - 9 for Jan - Sept, A B or C for Oct Nov & Dec

YY for 2 digit year

SSSS for serial number 0000 - 9999

Also, this ensures that there never a letter I or O.

This increases the total number of characters from 7 to 10.
{info}
{info}
&nbsp;
\\
\\]]></property>
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<id name="id">26673188</id>
<property name="body"><![CDATA[Our current (MBARI) puck count is [here|^2014_PUCK _INVENTORYv2.xlsx|MBARI puck count].
\\

Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note that we have yet to make a full batch of high-volume snap pucks, but when we do, those will be labeled 1HV (top and bottom).

Here is who is doing our etching:

LaserMark
2109 O'Toole Ave. Ste S
San Jose, CA 95131
Phone 408 433-9333
Fax 408 433-9343
\\
\\

Here is what I have packed up for etching:
| Type | Top/bottom | Numbered | Amount | NOTE |
| WCR | Top | 040-079 | 40 | \\ |
| \\ | Bottom | 040-079 | 40 | \\ |
| LAF | Top | 040-078 | 39 | 1=Missing |
| \\ | Bottom | 040-078 | 39 | 1=Missing |
| SAF | Top | 040-075 | 36 | 4sent to Gregg D |
| \\ | Bottom | 040-075 | 36 | 4sent to Gregg D |
| SHT | Top | 080-159 | 80 | \\ |
| SH1 | Bottom | 080-159 | 80 | \\ |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 390 | \\ |
\\
\\

I also sent 1 WCR puck (top&bottom) as a font sample.&nbsp; When these come back I will pack up the ones that are to be re-numbered(SHT2000-079).&nbsp; I haven't received a quote yet but Laser Mark said about $2 each piece + shipping.
\\

{color:#ff0000}UPDATE 3/24/08{color}

The SH1 tops that were misprinted are going to be sent out tomorrow to be re etched along with one of the LAF's that escaped detection last time:
| Type | Top/bottom | Numbered | Amount | NOTE |
| LAF | Top | 079 | 1 | Found the Lost 1\! |
| \\ | Bottom | 079 | 1 | \\ |
| SHT | Top | 000-079 | 80 | Old etching to be X'd out |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 82 | \\ |
That is all for now
\\
\\
\\

{color:#ff0000}UPDATE 2/24/09&nbsp; There have been several iterations of the above serialization process since this was last updated.{color}&nbsp;

Here is where we now stand:
| This   is an inventory of pucks that have been serialized and are available for   use.&nbsp; | \\ | \\ | \\ |
| There are   aprox. 1200 more pieces (or 600 more pucks) that have yet to be serialized. | \\ | \\ |
| They are   located in the 'B' building lab | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| Type | Top/Bottom | Lot 2 | Lot 2 | Lot 3 | Lot 3 | Lot 4 | Total | \\ |
| WCR | Top | 40 | 40 | 40 | 39 | 40 | 199 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 40 | 40 | 200 | \\ |
| LAF | Top | 40 | 40 | 40 | 38 | 40 | 198 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 36 | 40 | 196 | \\ |
| SAF | Top | 40 | 36 | 40 | 39 | 40 | 195 | \\ |
| \\ | Bottom | 40 | 36 | 40 | 40 | 40 | 196 | \\ |
| SHT | Top | 80 | 80 | 80 | 80 | 80 | 400 | \\ |
| SH1 \\ | Bottom | 80 | 80 | 80 | 77 | 80 | 397 | \\ |
| Total | \\ | 400 | 392 | 400 | 389 | 400 | 1981 | 990.5 |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | pieces | pucks |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| The   lot number refers to the 4th place in the serialization code:&nbsp; | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 letter type | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 1 digit lot number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 digit individual part number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| All parts   are numbered 000-079 ( except where some are missing) for each lot EXCEPT for : | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SHT=000-159 | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SH1=000-159 | \\ | \\ | \\ | \\ |
{color:#ff0000}{*}UPDATE August 11, 2010{*}{color}

&nbsp;Puck order from McLane arrived.

Rec'd&nbsp; 160 SH1, and 80 ea of LAF, SAF, WCR, HV (consists of HV top and SH1 bottom), all laser-etched.

PO 1010318
\\

Here is their email explaining their numbering system (sent Jan 14, 2010):
{Info:title=Mclane Numbering Scheme}
{Info}
From: Tim Shanahan \[mailto:tshanahan@mclanelabs.com\]
Sent: Thursday, January 14, 2010 8:52 AM
To: 'Birch, James'
Cc: 'Pargett, Douglas'; 'Jensen, Scott'; Everlove, Cheri; 'Scholin, Chris';
Yuki Honjo (yhonjo@mclanelabs.com); Ivory Engstrom
(iengstrom@mclanelabs.com); Mike Mathewson (mathewson@mclanelabs.com)
Subject: Puck serial number format

Hello All,

We've been thinking about the serial number format for the pucks and we'd
like to suggest some modifications.&nbsp; I'm concerned about duplicating lot
numbers and the potential for having runs bigger than 1000 units.

At least for now, I think there's the possibility of McLane and MBARI still
continuing to make puck independently.&nbsp; Keeping track of the current lot
number could be problematic.

So I propose the following:

TTTMYYSSSS

TTT for type code as below.

MYY for date code in
M= 1 - 9 for Jan - Sept, A B or C for Oct Nov & Dec

YY for 2 digit year

SSSS for serial number 0000 - 9999

Also, this ensures that there never a letter I or O.

This increases the total number of characters from 7 to 10.
{info}
{info}
&nbsp;
\\
\\]]></property>
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<property name="body"><![CDATA[h6.

*Jan 24, 2018*
Deploy Aku with Koa and 60 cartridge archival mission.&nbsp; Collecting \~32 samples for Ed and Kevan (eDNA), then running remainder (~19) as engineering tests with 20 minute filtering time-outs. ]]></property>
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<id name="id">26673187</id>
<property name="body"><![CDATA[Our current (MBARI) puck count is here.
\\

Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note that we have yet to make a full batch of high-volume snap pucks, but when we do, those will be labeled 1HV (top and bottom).

Here is who is doing our etching:

LaserMark
2109 O'Toole Ave. Ste S
San Jose, CA 95131
Phone 408 433-9333
Fax 408 433-9343
\\
\\

Here is what I have packed up for etching:
| Type | Top/bottom | Numbered | Amount | NOTE |
| WCR | Top | 040-079 | 40 | \\ |
| \\ | Bottom | 040-079 | 40 | \\ |
| LAF | Top | 040-078 | 39 | 1=Missing |
| \\ | Bottom | 040-078 | 39 | 1=Missing |
| SAF | Top | 040-075 | 36 | 4sent to Gregg D |
| \\ | Bottom | 040-075 | 36 | 4sent to Gregg D |
| SHT | Top | 080-159 | 80 | \\ |
| SH1 | Bottom | 080-159 | 80 | \\ |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 390 | \\ |
\\
\\

I also sent 1 WCR puck (top&bottom) as a font sample.&nbsp; When these come back I will pack up the ones that are to be re-numbered(SHT2000-079).&nbsp; I haven't received a quote yet but Laser Mark said about $2 each piece + shipping.
\\

{color:#ff0000}UPDATE 3/24/08{color}

The SH1 tops that were misprinted are going to be sent out tomorrow to be re etched along with one of the LAF's that escaped detection last time:
| Type | Top/bottom | Numbered | Amount | NOTE |
| LAF | Top | 079 | 1 | Found the Lost 1\! |
| \\ | Bottom | 079 | 1 | \\ |
| SHT | Top | 000-079 | 80 | Old etching to be X'd out |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 82 | \\ |
That is all for now
\\
\\
\\

{color:#ff0000}UPDATE 2/24/09&nbsp; There have been several iterations of the above serialization process since this was last updated.{color}&nbsp;

Here is where we now stand:
| This   is an inventory of pucks that have been serialized and are available for   use.&nbsp; | \\ | \\ | \\ |
| There are   aprox. 1200 more pieces (or 600 more pucks) that have yet to be serialized. | \\ | \\ |
| They are   located in the 'B' building lab | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| Type | Top/Bottom | Lot 2 | Lot 2 | Lot 3 | Lot 3 | Lot 4 | Total | \\ |
| WCR | Top | 40 | 40 | 40 | 39 | 40 | 199 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 40 | 40 | 200 | \\ |
| LAF | Top | 40 | 40 | 40 | 38 | 40 | 198 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 36 | 40 | 196 | \\ |
| SAF | Top | 40 | 36 | 40 | 39 | 40 | 195 | \\ |
| \\ | Bottom | 40 | 36 | 40 | 40 | 40 | 196 | \\ |
| SHT | Top | 80 | 80 | 80 | 80 | 80 | 400 | \\ |
| SH1 \\ | Bottom | 80 | 80 | 80 | 77 | 80 | 397 | \\ |
| Total | \\ | 400 | 392 | 400 | 389 | 400 | 1981 | 990.5 |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | pieces | pucks |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| The   lot number refers to the 4th place in the serialization code:&nbsp; | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 letter type | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 1 digit lot number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 digit individual part number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| All parts   are numbered 000-079 ( except where some are missing) for each lot EXCEPT for : | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SHT=000-159 | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SH1=000-159 | \\ | \\ | \\ | \\ |
{color:#ff0000}{*}UPDATE August 11, 2010{*}{color}

&nbsp;Puck order from McLane arrived.

Rec'd&nbsp; 160 SH1, and 80 ea of LAF, SAF, WCR, HV (consists of HV top and SH1 bottom), all laser-etched.

PO 1010318
\\

Here is their email explaining their numbering system (sent Jan 14, 2010):
{Info:title=Mclane Numbering Scheme}
{Info}
From: Tim Shanahan \[mailto:tshanahan@mclanelabs.com\]
Sent: Thursday, January 14, 2010 8:52 AM
To: 'Birch, James'
Cc: 'Pargett, Douglas'; 'Jensen, Scott'; Everlove, Cheri; 'Scholin, Chris';
Yuki Honjo (yhonjo@mclanelabs.com); Ivory Engstrom
(iengstrom@mclanelabs.com); Mike Mathewson (mathewson@mclanelabs.com)
Subject: Puck serial number format

Hello All,

We've been thinking about the serial number format for the pucks and we'd
like to suggest some modifications.&nbsp; I'm concerned about duplicating lot
numbers and the potential for having runs bigger than 1000 units.

At least for now, I think there's the possibility of McLane and MBARI still
continuing to make puck independently.&nbsp; Keeping track of the current lot
number could be problematic.

So I propose the following:

TTTMYYSSSS

TTT for type code as below.

MYY for date code in
M= 1 - 9 for Jan - Sept, A B or C for Oct Nov & Dec

YY for 2 digit year

SSSS for serial number 0000 - 9999

Also, this ensures that there never a letter I or O.

This increases the total number of characters from 7 to 10.
{info}
{info}
&nbsp;
\\
\\]]></property>
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</property>
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<id name="id">19073649</id>
<property name="body"><![CDATA[Back to basics ...

# What does the ESP do?
## Collects discrete water samples
## Concentrates microorganisms or particles
## Automates application of molecular probes which identify microorganisms and their gene products
## Archives samples for later analysis]]></property>
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</property>
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<id name="id">19073650</id>
<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.

June 26 - continues to run, but lost internet access due to an unknown networking error.

h3. {color:#ff00ff}So. California Deployment of ESP-Gordon / NEO{color}

Aug 30 \-\- Haul instrument and gear in trailer and MBARI van to deploy on OCSD R/V Nerissa.  Calm seas, hot weather, instrument in \~10:30am.  Gordon w/PCR, CTD, ISUS, cell-phone modem (T-Mobile).  Sewage diversion to begin Sep 11, 2012.

Kevan collecting data here: [http://www.stanford.edu/~kevany/ESP/].

Sep 14-noticed CTD battery draining faster than expected because of optode.&nbsp; Also, ATV encoder in MFB&nbsp; kept returning 511, which is 2**9-1&nbsp; meaning all bits are stuck high--typical way they fail.&nbsp; Stopped PCR, continued SHA, but with dead CTD no contextual data to adaptive sample off of.&nbsp; Decision to flip for NEO on Sep 26.

h3. {color:#ff00ff}Fall CANON--Drifter with ESP-Moe / Moe{color}

WF leaves MBARI Sept 10.&nbsp; Moe with PCR, ISUS, CTD, PAR, and buoy has downward ADCP.&nbsp; Roman and Julie R. on ship.

Moe went into water Sep 11. First phase slated for 6pm.

Pulled Sep 17 (10:30am).&nbsp; E/M cable started flaking out either due to connector or bad ethernet extender.&nbsp; Decision to end mission unrelated to this. ]]></property>
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<property name="body"><![CDATA[Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note that we have yet to make a full batch of high-volume snap pucks, but when we do, those will be labeled 1HV (top and bottom).

Here is who is doing our etching:

LaserMark
2109 O'Toole Ave. Ste S
San Jose, CA 95131
Phone 408 433-9333
Fax 408 433-9343
\\
\\

Here is what I have packed up for etching:
| Type | Top/bottom | Numbered | Amount | NOTE |
| WCR | Top | 040-079 | 40 | \\ |
| \\ | Bottom | 040-079 | 40 | \\ |
| LAF | Top | 040-078 | 39 | 1=Missing |
| \\ | Bottom | 040-078 | 39 | 1=Missing |
| SAF | Top | 040-075 | 36 | 4sent to Gregg D |
| \\ | Bottom | 040-075 | 36 | 4sent to Gregg D |
| SHT | Top | 080-159 | 80 | \\ |
| SH1 | Bottom | 080-159 | 80 | \\ |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 390 | \\ |
\\
\\

I also sent 1 WCR puck (top&bottom) as a font sample.&nbsp; When these come back I will pack up the ones that are to be re-numbered(SHT2000-079).&nbsp; I haven't received a quote yet but Laser Mark said about $2 each piece + shipping.
\\

{color:#ff0000}UPDATE 3/24/08{color}

The SH1 tops that were misprinted are going to be sent out tomorrow to be re etched along with one of the LAF's that escaped detection last time:
| Type | Top/bottom | Numbered | Amount | NOTE |
| LAF | Top | 079 | 1 | Found the Lost 1\! |
| \\ | Bottom | 079 | 1 | \\ |
| SHT | Top | 000-079 | 80 | Old etching to be X'd out |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 82 | \\ |
That is all for now
\\
\\
\\

{color:#ff0000}UPDATE 2/24/09&nbsp; There have been several iterations of the above serialization process since this was last updated.{color}&nbsp;

Here is where we now stand:
| This   is an inventory of pucks that have been serialized and are available for   use.&nbsp; | \\ | \\ | \\ |
| There are   aprox. 1200 more pieces (or 600 more pucks) that have yet to be serialized. | \\ | \\ |
| They are   located in the 'B' building lab | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| Type | Top/Bottom | Lot 2 | Lot 2 | Lot 3 | Lot 3 | Lot 4 | Total | \\ |
| WCR | Top | 40 | 40 | 40 | 39 | 40 | 199 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 40 | 40 | 200 | \\ |
| LAF | Top | 40 | 40 | 40 | 38 | 40 | 198 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 36 | 40 | 196 | \\ |
| SAF | Top | 40 | 36 | 40 | 39 | 40 | 195 | \\ |
| \\ | Bottom | 40 | 36 | 40 | 40 | 40 | 196 | \\ |
| SHT | Top | 80 | 80 | 80 | 80 | 80 | 400 | \\ |
| SH1 \\ | Bottom | 80 | 80 | 80 | 77 | 80 | 397 | \\ |
| Total | \\ | 400 | 392 | 400 | 389 | 400 | 1981 | 990.5 |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | pieces | pucks |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| The   lot number refers to the 4th place in the serialization code:&nbsp; | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 letter type | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 1 digit lot number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 digit individual part number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| All parts   are numbered 000-079 ( except where some are missing) for each lot EXCEPT for : | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SHT=000-159 | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SH1=000-159 | \\ | \\ | \\ | \\ |
{color:#ff0000}{*}UPDATE August 11, 2010{*}{color}

&nbsp;Puck order from McLane arrived.

Rec'd&nbsp; 160 SH1, and 80 ea of LAF, SAF, WCR, HV (consists of HV top and SH1 bottom), all laser-etched.

PO 1010318
\\

Here is their email explaining their numbering system (sent Jan 14, 2010):
{Info:title=Mclane Numbering Scheme}
{Info}
From: Tim Shanahan \[mailto:tshanahan@mclanelabs.com\]
Sent: Thursday, January 14, 2010 8:52 AM
To: 'Birch, James'
Cc: 'Pargett, Douglas'; 'Jensen, Scott'; Everlove, Cheri; 'Scholin, Chris';
Yuki Honjo (yhonjo@mclanelabs.com); Ivory Engstrom
(iengstrom@mclanelabs.com); Mike Mathewson (mathewson@mclanelabs.com)
Subject: Puck serial number format

Hello All,

We've been thinking about the serial number format for the pucks and we'd
like to suggest some modifications.&nbsp; I'm concerned about duplicating lot
numbers and the potential for having runs bigger than 1000 units.

At least for now, I think there's the possibility of McLane and MBARI still
continuing to make puck independently.&nbsp; Keeping track of the current lot
number could be problematic.

So I propose the following:

TTTMYYSSSS

TTT for type code as below.

MYY for date code in
M= 1 - 9 for Jan - Sept, A B or C for Oct Nov & Dec

YY for 2 digit year

SSSS for serial number 0000 - 9999

Also, this ensures that there never a letter I or O.

This increases the total number of characters from 7 to 10.
{info}
{info}
&nbsp;
\\
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<property name="body"><![CDATA[h4. (as of April, 2015)


h1. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

*21.5m (BAD)*
Now with bad connector...&nbsp;
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos in the attachments of this page.

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)

*15.2m (BAD; bad BSR?)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]

(shockles 1-4 used in SoCal ECOHAB-2013 and Monterey Bay ECOHAB-2013, but unclear which used when )

h4. ESP-001 (modified with 'stretchier' cord)


* 44 days during Catalina (April 2014) deployment
* Moran MB deployment (Sep/Oct 2014)
* ECOHAB?

h4. ESP-002

\\

h4. ESP-003

* &nbsp;32 days S. Cal ECOHAB w/Mack (Apr 2014)

h4. ESP-004

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).

h4. ESP-005


h1. Anchor lines

\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4.


h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\
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<property name="body"><![CDATA[h4. (as of April, 2015)


h1. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

*21.5m (BAD)*
Now with bad connector...&nbsp;
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos in the attachments of this page.

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)

*15.2m (BAD; bad BSR?)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]

(shockles 1-4 used in SoCal ECOHAB-2013 and Monterey Bay ECOHAB-2013, but unclear which used when )

h4. ESP-001

* 44 days during Catalina (April 2014) deployment
* Moran MB deployment (Sep/Oct 2014)

h4. ESP-002

\\

h4. ESP-003

* &nbsp;32 days S. Cal ECOHAB w/Mack (Apr 2014)

h4. ESP-004

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).

h4. ESP-005


h1. Anchor lines

\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4.


h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\
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<property name="body"><![CDATA[Present: Scott, Doug, Chris S., Jim, Wayne, Brent, Kevin
Absent: Cheri (SolidWorks training), Addie (maternity)


h3.


h3. Machine Builds

* &nbsp;o-ring test out.&nbsp; No results yet.&nbsp; O-ring in Mack was not sealing properly; needs exploring/explanation.
* Pucks.&nbsp; Have one set left to be etched, which will give us 4 complete snap-puck sets; all same rev, but different lots.

h3. MFB

* Getting close to the end of the 2-grill build.&nbsp; 1 has had fluidics checked out; both have syringe and heaters calibrated
* Chris P running dye test on MFB01 now, may try and run PCR tomorrow
* Tomorrow AM will meet with McLane and map out the concepts of a visit for the core build.

h3. Software

* &nbsp;Moving from development mode to more a manufacturing mode has caused Brent to re-jigger the config files on both the Core and MFB's.&nbsp; Each now has a PreConfig.RB, Config.RB, and PostConfig.RB, with the pre\- and post\- common to ALL MFB's; the Config.RB is unique to each unit.&nbsp; This change is also being implemented on the cores.
* Brent has discovered a file accessing issue with the CTD that will require Bob Herlien's help for a week in early 2009.&nbsp; This should stop the hiccup we've seen when hooking up new CTD's to the core(s).
* Xylinx issue still causing heartburn.&nbsp; Now using old code, with both old or new compilers, produces corrupted results.&nbsp; It has worked for many years, but now is flaking on us.&nbsp; Wayne to delve into what is going on--this is top priority since DWSM uses these same xylinx boards for quadrature decoding.

h3. DWSM


h6. +Sphere+

* Chris S. has found that near-term 2500m is max depth we may want to go.&nbsp; He has found that depth certification is very strict if Alvin will be near it (test at 150% 10x then hold 1hr at max).&nbsp; Much discussion on whether this is necessary, what would we need Alvin for, the need for a manual release.&nbsp; We want to go to maximum depth, but don't want the setup to become an engineering project in itself.
* DECISION:&nbsp; we will outfit w/ strain guages and go to maximum (either of the test facility or to 3750m)
* Will get quotes from both Southwest and Port Heuneme;&nbsp; Will try and have tested in January.

h6. +Elevator+

* Have learned that prime real estate near MARS has already been taken, so we will need some type of long or extension cable, which may impact elevator design.
* CDR will be Wednesday (December 17).&nbsp; Jim will schedule

*{+}DWSM{+}*
* No work since last week

h3. GUI Development

* &nbsp;Kevin has tuaght Roman M. how to download data, which he has done for the last triple-deployemnt.

h3. Other Items:

* &nbsp;Discussed potential classes at JALA for Brent and Scott. Both will be going, with perhaps 2 science people.&nbsp; Must get logistics to Cindy by tomorrow.
* Chris has spoken to Grech about moving ship days and not looking good.&nbsp; Solution will be to move Feb and Aug orphan days to the Fall for another MARS hookup.&nbsp; Although no extended running time before Flyer cruise in June, his deemed acceptable. Dates now look like this:
*** Dive 1:&nbsp; March 25--no core but elevator, DWSM, sphere
*** Dive 2:&nbsp; April 7-core in sphere, elevator, DWSM-run WCR
*** Dive 3:&nbsp; April 14-core in sphere, elevator, DWSM-minimal chemistry (SHA)
*** JUNE 8-12--Flyer cruise (these dates may be moved a few days earlier, depending on DMO scheduling changes)
*** AUG 16-26--Flyer to Axial
*** Dive 4:&nbsp; Fall #1 \-plug into MARS (date depends on what we can get that first week)
*** Dive 5:&nbsp; Fall&nbsp; #2\- pick up from MARS
*** Dive 6: Nov 4--plug into MARS, pickup in early 2010]]></property>
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# [10Apr2008]
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# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
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# [02Oct2008] (Pre-deployment discussions)
# [09Oct2008] (the day after deployment....)
# [16Oct2008]
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# [30Oct2008]
# [06Nov2008]
# [13Nov2008]
# [20Nov2008] (Scott's in charge)
# 27Nov2008 (no mtg--Thanksgiving)
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# [11Dec2008]]]></property>
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# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
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# [09Oct2008] (the day after deployment....)
# [16Oct2008]
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# [30Oct2008]
# [06Nov2008]
# [13Nov2008]
# [20Nov2008] (Scott's in charge)
# 27Nov2008 (no mtg--Thanksgiving)
# [04Dec2008]
# [11Dec2008]
# [18Dec2008] (Brent's in charge)]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15-18, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;

*Jun 6, 2017*

Rich Walsh of SCRIPPS went to buoy and swapped the non-working MELO with a newer one that we had sent down.&nbsp; We are now getting hourly (correct) positions.\\

h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 27\- May 8, 2017*

This was part of a 5-vehicle launch (Tethys, Daphne, Aku w/ ESP Honu, Ahi, Opah).&nbsp; Gabe Foreman arrived from UH to help with piloting.&nbsp; Adam Jones helped launch Aku and Opah.

Ran multiple simulation to test the mission.

On Weds, May 3, tried first 'real' concurrent sampling.&nbsp; Cartridge 1 threw an alignment error--could not push on plunge valve.&nbsp; We labeled that cartridge 'wet' and moved to cartridge 2.&nbsp; But this notification not written to file, and was lost when power was cycled.&nbsp; Thus, we thought we were onto cartridge #2, but in reality were on #1 (which started working....).&nbsp; Sampling was as follows:

&nbsp;All cartridges started filtering at 60m depth while vehicle ascended to surface, where filtering stopped.&nbsp; WF took CTD casts in the same area at same time.&nbsp; Kevan took 2L each from each of these bottles: 60m, 40m, 20m, 10m, surface and mixed the 10L in a carboy.&nbsp; From that carboy, he sampled 1L through a cartridge on tackle-box, and 1L (x3) on peristaltic.&nbsp; Sample #2 had 1L (x3) through the tacklebox cartridge.&nbsp; Francisco took 1L from each of those depths and peristaltic filtered.

&nbsp;Because of the cartridge number mix-up, Honu returned with a dry #5 cartridge, which we ran as a negative control in the lab.&nbsp; Investigation of the alignment issues is ongoing.
\\

h3. Summary of 3G flights to this point (May 2017):

{panel}
*Nov* {color:#0000ff}2014{color} &nbsp;
Very first 3G flight.&nbsp; Makai with one Archive cartridge.&nbsp; Mission lasted \~3 days.
\_____________________\_
*July* {color:#0000ff}2015{color} &nbsp;
First 5-cartridge flight on Makai.&nbsp; All Archive.&nbsp; Cartridge 1 toroid valve stuck in bypass mode, thus recovered only 4 sample filters.&nbsp; All collected <20m deep.

*Dec* {color:#0000ff}2015{color} &nbsp;
First 4 & 1 (archive/LnG) flight on Makai.&nbsp; Many vehicle errors.&nbsp; No stratification so difficult to find any 'features'.&nbsp; Acquired 2 archives and 1 LnG.&nbsp; rough weather recovery.&nbsp; I don't have actual collection depths for these three samples.
\_____________________\_
*Feb* {color:#0000ff}2016{color} &nbsp;
Repeat Dec flight.&nbsp; 1 LnG fired first, then 4 Archives on Makai.&nbsp; Samples taken at 8.7m, 12.7m, 13m, 27m, and 27m.

*Dec* {color:#0000ff}2016{color} &nbsp;
Depth testing with Honu in Makai.&nbsp; 5 archival cartridges.&nbsp; Fired at chl max (~14m), 50m, and 100m.&nbsp; 200m cartridge started, but vehicle cut ESP power before finished.&nbsp; 300m sample had carousel alignment issue and did not complete.&nbsp; 3 of 5 samples preserved.
\_____________________\_
*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; meet with R/V Shimada (CALCOFI ship).&nbsp; Difficulties with water in payload section and rough recovery.&nbsp; Three filters recovered (chl-max to compare to Shimada's, and two at 10m)

*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; CANON cruise and WF rendezvous.&nbsp; Alignment problem had us bypass (so we thought) cartridge #1.&nbsp; Four archives collected, two a smear from 40m to surface, two from 60m to surface.&nbsp; These are matched to ship samples Kevan collected.
\_____________________\_

Overall, we have 21 archival filters that correctly filtered and preserved samples; two LnG samples were collected (were both run through SPR on the vehicle?)
{panel}

h3.]]></property>
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<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.

June 26 - continues to run, but lost internet access due to an unknown networking error.

h3. {color:#ff00ff}So. California Deployment of ESP-Gordon / NEO{color}

Aug 30 \-\- Haul instrument and gear in trailer and MBARI van to deploy on OCSD R/V Nerissa.  Calm seas, hot weather, instrument in \~10:30am.  Gordon w/PCR, CTD, ISUS, cell-phone modem (T-Mobile).  Sewage diversion to begin Sep 11, 2012.

Kevan collecting data here: [http://www.stanford.edu/~kevany/ESP/].

Sep 14--noticed CTD battery draining faster than expected because of optode.&nbsp; Also, ATV encoder in MFB&nbsp; kept returning 511, which is 2**9-1&nbsp; meaning all bits are stuck high---typical way they fail.&nbsp; Stopped PCR, continued SHA, but with dead CTD no contextual data to adaptive sample off of.&nbsp; Decision to flip for NEO on Sep 26.


h3. {color:#ff00ff}Fall CANON--Drifter with ESP-Moe / Moe{color}

WF leaves MBARI Sept 10.&nbsp; Moe with PCR, ISUS, CTD, PAR, and buoy has downward ADCP.&nbsp; Roman and Julie R. on ship.

Moe went into water Sep 11. First phase slated for 6pm.

Pulled Sep 17 (10:30am).&nbsp; E/M cable started flaking out either due to connector or bad ethernet extender.&nbsp; Decision to end mission unrelated to this. ]]></property>
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<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.

June 26 - continues to run, but lost internet access due to an unknown networking error.

h3. {color:#ff00ff}So. California Deployment of ESP-Gordon / NEO{color}

Aug 30 \-\- Haul instrument and gear in trailer and MBARI van to deploy on OCSD R/V Nerissa.  Calm seas, hot weather, instrument in \~10:30am.  Gordon w/PCR, CTD, ISUS, cell-phone modem (T-Mobile).  Sewage diversion to begin Sep 11, 2012.

Kevan collecting data here: http://www.stanford.edu/~kevany/ESP/.


h3. {color:#ff00ff}Fall CANON--Drifter with ESP-Moe / Moe{color}

WF leaves MBARI Sept 10.&nbsp; Moe with PCR, ISUS, CTD, PAR, and buoy has downward ADCP.&nbsp; Roman and Julie R. on ship.

Moe went into water Sep 11. First phase slated for 6pm.]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15-18, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;

*Jun 6, 2017*

Rich Walsh of SCRIPPS went to buoy and swapped the non-working MELO with a newer one that we had sent down.&nbsp; We are now getting hourly (correct) positions.

*Sept 6, 2017*

Final recovery of Waldo.


h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 27\- May 8, 2017*

This was part of a 5-vehicle launch (Tethys, Daphne, Aku w/ ESP Honu, Ahi, Opah).&nbsp; Gabe Foreman arrived from UH to help with piloting.&nbsp; Adam Jones helped launch Aku and Opah.

Ran multiple simulation to test the mission.

On Weds, May 3, tried first 'real' concurrent sampling.&nbsp; Cartridge 1 threw an alignment error--could not push on plunge valve.&nbsp; We labeled that cartridge 'wet' and moved to cartridge 2.&nbsp; But this notification not written to file, and was lost when power was cycled.&nbsp; Thus, we thought we were onto cartridge #2, but in reality were on #1 (which started working....).&nbsp; Sampling was as follows:

&nbsp;All cartridges started filtering at 60m depth while vehicle ascended to surface, where filtering stopped.&nbsp; WF took CTD casts in the same area at same time.&nbsp; Kevan took 2L each from each of these bottles: 60m, 40m, 20m, 10m, surface and mixed the 10L in a carboy.&nbsp; From that carboy, he sampled 1L through a cartridge on tackle-box, and 1L (x3) on peristaltic.&nbsp; Sample #2 had 1L (x3) through the tacklebox cartridge.&nbsp; Francisco took 1L from each of those depths and peristaltic filtered.

&nbsp;Because of the cartridge number mix-up, Honu returned with a dry #5 cartridge, which we ran as a negative control in the lab.&nbsp; Investigation of the alignment issues is ongoing.
\\

h3. Summary of 3G flights to this point (May 2017):

{panel}
*Nov* {color:#0000ff}2014{color} &nbsp;
Very first 3G flight.&nbsp; Makai with one Archive cartridge.&nbsp; Mission lasted \~3 days.
\_____________________\_
*July* {color:#0000ff}2015{color} &nbsp;
First 5-cartridge flight on Makai.&nbsp; All Archive.&nbsp; Cartridge 1 toroid valve stuck in bypass mode, thus recovered only 4 sample filters.&nbsp; All collected <20m deep.

*Dec* {color:#0000ff}2015{color} &nbsp;
First 4 & 1 (archive/LnG) flight on Makai.&nbsp; Many vehicle errors.&nbsp; No stratification so difficult to find any 'features'.&nbsp; Acquired 2 archives and 1 LnG.&nbsp; rough weather recovery.&nbsp; I don't have actual collection depths for these three samples.
\_____________________\_
*Feb* {color:#0000ff}2016{color} &nbsp;
Repeat Dec flight.&nbsp; 1 LnG fired first, then 4 Archives on Makai.&nbsp; Samples taken at 8.7m, 12.7m, 13m, 27m, and 27m.

*Dec* {color:#0000ff}2016{color} &nbsp;
Depth testing with Honu in Makai.&nbsp; 5 archival cartridges.&nbsp; Fired at chl max (~14m), 50m, and 100m.&nbsp; 200m cartridge started, but vehicle cut ESP power before finished.&nbsp; 300m sample had carousel alignment issue and did not complete.&nbsp; 3 of 5 samples preserved.
\_____________________\_
*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; meet with R/V Shimada (CALCOFI ship).&nbsp; Difficulties with water in payload section and rough recovery.&nbsp; Three filters recovered (chl-max to compare to Shimada's, and two at 10m)

*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; CANON cruise and WF rendezvous.&nbsp; Alignment problem had us bypass (so we thought) cartridge #1.&nbsp; Four archives collected, two a smear from 40m to surface, two from 60m to surface.&nbsp; These are matched to ship samples Kevan collected.
\_____________________\_

Overall, we have 21 archival filters that correctly filtered and preserved samples; two LnG samples were collected (were both run through SPR on the vehicle?)
{panel}

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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15-18, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;

*Jun 6, 2017*

Rich Walsh of SCRIPPS went to buoy and swapped the non-working MELO with a newer one that we had sent down.&nbsp; We are now getting hourly (correct) positions.

*Sept 6, 2017*

Final recovery of Waldo.

h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 27\- May 8, 2017*

This was part of a 5-vehicle launch (Tethys, Daphne, Aku w/ ESP Honu, Ahi, Opah).&nbsp; Gabe Foreman arrived from UH to help with piloting.&nbsp; Adam Jones helped launch Aku and Opah.

Ran multiple simulation to test the mission.

On Weds, May 3, tried first 'real' concurrent sampling.&nbsp; Cartridge 1 threw an alignment error--could not push on plunge valve.&nbsp; We labeled that cartridge 'wet' and moved to cartridge 2.&nbsp; But this notification not written to file, and was lost when power was cycled.&nbsp; Thus, we thought we were onto cartridge #2, but in reality were on #1 (which started working....).&nbsp; Sampling was as follows:

&nbsp;All cartridges started filtering at 60m depth while vehicle ascended to surface, where filtering stopped.&nbsp; WF took CTD casts in the same area at same time.&nbsp; Kevan took 2L each from each of these bottles: 60m, 40m, 20m, 10m, surface and mixed the 10L in a carboy.&nbsp; From that carboy, he sampled 1L through a cartridge on tackle-box, and 1L (x3) on peristaltic.&nbsp; Sample #2 had 1L (x3) through the tacklebox cartridge.&nbsp; Francisco took 1L from each of those depths and peristaltic filtered.

&nbsp;Because of the cartridge number mix-up, Honu returned with a dry #5 cartridge, which we ran as a negative control in the lab.&nbsp; Investigation of the alignment issues is ongoing.
\\

h3. Summary of 3G flights to this point (May 2017):

{panel}
*Nov* {color:#0000ff}2014{color} &nbsp;
Very first 3G flight.&nbsp; Makai with one Archive cartridge.&nbsp; Mission lasted \~3 days.
\_____________________\_
*July* {color:#0000ff}2015{color} &nbsp;
First 5-cartridge flight on Makai.&nbsp; All Archive.&nbsp; Cartridge 1 toroid valve stuck in bypass mode, thus recovered only 4 sample filters.&nbsp; All collected <20m deep.

*Dec* {color:#0000ff}2015{color} &nbsp;
First 4 & 1 (archive/LnG) flight on Makai.&nbsp; Many vehicle errors.&nbsp; No stratification so difficult to find any 'features'.&nbsp; Acquired 2 archives and 1 LnG.&nbsp; rough weather recovery.&nbsp; I don't have actual collection depths for these three samples.
\_____________________\_
*Feb* {color:#0000ff}2016{color} &nbsp;
Repeat Dec flight.&nbsp; 1 LnG fired first, then 4 Archives on Makai.&nbsp; Samples taken at 8.7m, 12.7m, 13m, 27m, and 27m.

*Dec* {color:#0000ff}2016{color} &nbsp;
Depth testing with Honu in Makai.&nbsp; 5 archival cartridges.&nbsp; Fired at chl max (~14m), 50m, and 100m.&nbsp; 200m cartridge started, but vehicle cut ESP power before finished.&nbsp; 300m sample had carousel alignment issue and did not complete.&nbsp; 3 of 5 samples preserved.
\_____________________\_
*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; meet with R/V Shimada (CALCOFI ship).&nbsp; Difficulties with water in payload section and rough recovery.&nbsp; Three filters recovered (chl-max to compare to Shimada's, and two at 10m)

*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; CANON cruise and WF rendezvous.&nbsp; Alignment problem had us bypass (so we thought) cartridge #1.&nbsp; Four archives collected, two a smear from 40m to surface, two from 60m to surface.&nbsp; These are matched to ship samples Kevan collected.
\_____________________\_

Overall, we have 21 archival filters that correctly filtered and preserved samples; two LnG samples were collected (were both run through SPR on the vehicle?)
{panel}

h4. {color:#ff00cc}Makai flight w ESP-Koa and 60 Archive Cartridges{color}

*Dec 12 - xxx, 2017*

We decided to generate 5 'blocks' of behavior (below) each testing a certain collection scheme, with replicates.&nbsp; Combined samples for Ed with samples for eDNA work.


Out of 60 cartridges, 15 are controls (9 pre-experiment + 6 post-experiment); 45 will be fired offshore.
The 45 field samples are divided into 5 blocks, each block containing 9 samples.
In each 9-sample block, firings are in triplicate bursts: 1, 2, 3 in one continuous burst; then 4, 5, 6; and then 7, 8, 9.

Scientists and engineers will jointly select appropriate sampling locations in consideration of oceanographic features as well as LRAUV operation safety.

Block 1 (Bathymetry alert due to deep sampling):
Mission file: chlpeak_sampling_InAboveBelow.xml, in donut mode.
Initial horizontal search for high chl in local area; set the hi-chl spot as the sampling location; run a cylinder around sampling location
3 samples at vertical chl peak depth
3 samples at 100m depth
3 samples at 250m depth
Total: 9 samples, \~15 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time).

Block 2 (Bathymetry alert due to deep sampling):
Mission file: smear_sampling.xml, in donut mode.
3 samples smearing between 5m and 100m depths
3 samples at 100m depth
3 samples at 5m depth
Total: 9 samples, \~14 hours (presuming 1hr filtration time + 0.5hr processing time for each sample)

Block 3:
Mission file: isotherm_sampling.xml, in donut mode.
Initial horizontal search for high chl in local area; set the hi-chl spot as the sampling location; run a cylinder around sampling location
3 samples at the temperature corresponding to the vertical chl peak.
3 samples at chlpeak temp - deltaT1
3 samples at chlpeak temp + deltaT2
Total: 9 samples, \~15 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time).

Block 4:
Mission file: chlpeak_sampling_InAboveBelow.xml.xml, in drift mode.
Initial horizontal search for high chl in local area; set the hi-chl spot as the sampling location; run a cylinder around sampling location
3 samples at chl peak depth
Vertical perturbation to reacquire chl peak
3 samples at chl peak depth
Vertical perturbation to reacquire chl peak
3 samples at chl peak depth
Total: 9 samples, \~16 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time + vertical perturbation time).

Block 5:
Mission file: depth_sequence_sampling.xml, in donut mode
Scientists determine a horizontal feature, and set a certain depth for sampling
3 samples at the set depth on one side of feature
3 samples at same depth in feature
3 samples at same depth on other side of feature
Total: 9 samples, \~16 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + transit time)

\\

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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15-18, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;

*Jun 6, 2017*

Rich Walsh of SCRIPPS went to buoy and swapped the non-working MELO with a newer one that we had sent down.&nbsp; We are now getting hourly (correct) positions.

*Sept 6, 2017*

Final recovery of Waldo.

h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 27\- May 8, 2017*

This was part of a 5-vehicle launch (Tethys, Daphne, Aku w/ ESP Honu, Ahi, Opah).&nbsp; Gabe Foreman arrived from UH to help with piloting.&nbsp; Adam Jones helped launch Aku and Opah.

Ran multiple simulation to test the mission.

On Weds, May 3, tried first 'real' concurrent sampling.&nbsp; Cartridge 1 threw an alignment error--could not push on plunge valve.&nbsp; We labeled that cartridge 'wet' and moved to cartridge 2.&nbsp; But this notification not written to file, and was lost when power was cycled.&nbsp; Thus, we thought we were onto cartridge #2, but in reality were on #1 (which started working....).&nbsp; Sampling was as follows:

&nbsp;All cartridges started filtering at 60m depth while vehicle ascended to surface, where filtering stopped.&nbsp; WF took CTD casts in the same area at same time.&nbsp; Kevan took 2L each from each of these bottles: 60m, 40m, 20m, 10m, surface and mixed the 10L in a carboy.&nbsp; From that carboy, he sampled 1L through a cartridge on tackle-box, and 1L (x3) on peristaltic.&nbsp; Sample #2 had 1L (x3) through the tacklebox cartridge.&nbsp; Francisco took 1L from each of those depths and peristaltic filtered.

&nbsp;Because of the cartridge number mix-up, Honu returned with a dry #5 cartridge, which we ran as a negative control in the lab.&nbsp; Investigation of the alignment issues is ongoing.
\\

h3. Summary of 3G flights to this point (May 2017):

{panel}
*Nov* {color:#0000ff}2014{color} &nbsp;
Very first 3G flight.&nbsp; Makai with one Archive cartridge.&nbsp; Mission lasted \~3 days.
\_____________________\_
*July* {color:#0000ff}2015{color} &nbsp;
First 5-cartridge flight on Makai.&nbsp; All Archive.&nbsp; Cartridge 1 toroid valve stuck in bypass mode, thus recovered only 4 sample filters.&nbsp; All collected <20m deep.

*Dec* {color:#0000ff}2015{color} &nbsp;
First 4 & 1 (archive/LnG) flight on Makai.&nbsp; Many vehicle errors.&nbsp; No stratification so difficult to find any 'features'.&nbsp; Acquired 2 archives and 1 LnG.&nbsp; rough weather recovery.&nbsp; I don't have actual collection depths for these three samples.
\_____________________\_
*Feb* {color:#0000ff}2016{color} &nbsp;
Repeat Dec flight.&nbsp; 1 LnG fired first, then 4 Archives on Makai.&nbsp; Samples taken at 8.7m, 12.7m, 13m, 27m, and 27m.

*Dec* {color:#0000ff}2016{color} &nbsp;
Depth testing with Honu in Makai.&nbsp; 5 archival cartridges.&nbsp; Fired at chl max (~14m), 50m, and 100m.&nbsp; 200m cartridge started, but vehicle cut ESP power before finished.&nbsp; 300m sample had carousel alignment issue and did not complete.&nbsp; 3 of 5 samples preserved.
\_____________________\_
*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; meet with R/V Shimada (CALCOFI ship).&nbsp; Difficulties with water in payload section and rough recovery.&nbsp; Three filters recovered (chl-max to compare to Shimada's, and two at 10m)

*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; CANON cruise and WF rendezvous.&nbsp; Alignment problem had us bypass (so we thought) cartridge #1.&nbsp; Four archives collected, two a smear from 40m to surface, two from 60m to surface.&nbsp; These are matched to ship samples Kevan collected.
\_____________________\_

Overall, we have 21 archival filters that correctly filtered and preserved samples; two LnG samples were collected (were both run through SPR on the vehicle?)
{panel}

h4. {color:#ff00cc}Makai flight w ESP-Koa and 60 Archive Cartridges{color}

*Dec 12 - 20, 2017*

We decided to generate 5 'blocks' of behavior (below) each testing a certain collection scheme, with replicates.&nbsp; Combined samples for Ed with samples for eDNA work.

Out of 60 cartridges, 15 are controls (9 pre-experiment + 6 post-experiment); 45 will be fired offshore.
The 45 field samples are divided into 5 blocks, each block containing 9 samples.
In each 9-sample block, firings are in triplicate bursts: 1, 2, 3 in one continuous burst; then 4, 5, 6; and then 7, 8, 9.

Scientists and engineers will jointly select appropriate sampling locations in consideration of oceanographic features as well as LRAUV operation safety.

Block 1 (Bathymetry alert due to deep sampling):
Mission file: chlpeak_sampling_InAboveBelow.xml, in donut mode.
Initial horizontal search for high chl in local area; set the hi-chl spot as the sampling location; run a cylinder around sampling location
3 samples at vertical chl peak depth
3 samples at 100m depth
3 samples at 250m depth
Total: 9 samples, \~15 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time).

Block 2 (Bathymetry alert due to deep sampling):
Mission file: smear_sampling.xml, in donut mode.
3 samples smearing between 5m and 100m depths
3 samples at 100m depth
3 samples at 5m depth
Total: 9 samples, \~14 hours (presuming 1hr filtration time + 0.5hr processing time for each sample)

Block 3:
Mission file: isotherm_sampling.xml, in donut mode.
Initial horizontal search for high chl in local area; set the hi-chl spot as the sampling location; run a cylinder around sampling location
3 samples at the temperature corresponding to the vertical chl peak.
3 samples at chlpeak temp - deltaT1
3 samples at chlpeak temp + deltaT2
Total: 9 samples, \~15 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time).

Block 4:
Mission file: chlpeak_sampling_InAboveBelow.xml.xml, in drift mode.
Initial horizontal search for high chl in local area; set the hi-chl spot as the sampling location; run a cylinder around sampling location
3 samples at chl peak depth
Vertical perturbation to reacquire chl peak
3 samples at chl peak depth
Vertical perturbation to reacquire chl peak
3 samples at chl peak depth
Total: 9 samples, \~16 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time + vertical perturbation time).

Block 5:
Mission file: depth_sequence_sampling.xml, in donut mode
Scientists determine a horizontal feature, and set a certain depth for sampling
3 samples at the set depth on one side of feature
3 samples at same depth in feature
3 samples at same depth on other side of feature
Total: 9 samples, \~16 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + transit time)

\\

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<property name="body"><![CDATA[h2. Quotes

* Sphere casting [(Wah Chang)|^Wah Chang quote MBARI 60200 11-14 C5.pdf] \[1st piece arrived May 7, 2008\]
* Machining
** [Tapemation|^Tapemation quote MBARI 4K Hemi.doc]
** Hanard Machine (sent for quote 11-15-07 \--> [negative response])
** Sphere pictures are [here|\\Tornado\projectlibrary\ESP\DWSM\4k DWSM\Solidworks files\Elevator\tallhexman.tif]]]></property>
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<property name="body"><![CDATA[h2. Quotes

* Sphere casting [(Wah Chang)|^Wah Chang quote MBARI 60200 11-14 C5.pdf] \[1st piece arrived May 7, 2008\]
* Machining
** [Tapemation|^Tapemation quote MBARI 4K Hemi.doc]
** Hanard Machine (sent for quote 11-15-07 \--> [negative response])]]></property>
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<property name="body"><![CDATA[{mockup:testmock|2}

h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 15 Sep 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2015Sep08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15-18, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;

*Jun 6, 2017*

Rich Walsh of SCRIPPS went to buoy and swapped the non-working MELO with a newer one that we had sent down.&nbsp; We are now getting hourly (correct) positions.

*Sept 6, 2017*

Final recovery of Waldo.

h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 27\- May 8, 2017*

This was part of a 5-vehicle launch (Tethys, Daphne, Aku w/ ESP Honu, Ahi, Opah).&nbsp; Gabe Foreman arrived from UH to help with piloting.&nbsp; Adam Jones helped launch Aku and Opah.

Ran multiple simulation to test the mission.

On Weds, May 3, tried first 'real' concurrent sampling.&nbsp; Cartridge 1 threw an alignment error--could not push on plunge valve.&nbsp; We labeled that cartridge 'wet' and moved to cartridge 2.&nbsp; But this notification not written to file, and was lost when power was cycled.&nbsp; Thus, we thought we were onto cartridge #2, but in reality were on #1 (which started working....).&nbsp; Sampling was as follows:

&nbsp;All cartridges started filtering at 60m depth while vehicle ascended to surface, where filtering stopped.&nbsp; WF took CTD casts in the same area at same time.&nbsp; Kevan took 2L each from each of these bottles: 60m, 40m, 20m, 10m, surface and mixed the 10L in a carboy.&nbsp; From that carboy, he sampled 1L through a cartridge on tackle-box, and 1L (x3) on peristaltic.&nbsp; Sample #2 had 1L (x3) through the tacklebox cartridge.&nbsp; Francisco took 1L from each of those depths and peristaltic filtered.

&nbsp;Because of the cartridge number mix-up, Honu returned with a dry #5 cartridge, which we ran as a negative control in the lab.&nbsp; Investigation of the alignment issues is ongoing.
\\

h3. Summary of 3G flights to this point (May 2017):

{panel}
*Nov* {color:#0000ff}2014{color} &nbsp;
Very first 3G flight.&nbsp; Makai with one Archive cartridge.&nbsp; Mission lasted \~3 days.
\_____________________\_
*July* {color:#0000ff}2015{color} &nbsp;
First 5-cartridge flight on Makai.&nbsp; All Archive.&nbsp; Cartridge 1 toroid valve stuck in bypass mode, thus recovered only 4 sample filters.&nbsp; All collected <20m deep.

*Dec* {color:#0000ff}2015{color} &nbsp;
First 4 & 1 (archive/LnG) flight on Makai.&nbsp; Many vehicle errors.&nbsp; No stratification so difficult to find any 'features'.&nbsp; Acquired 2 archives and 1 LnG.&nbsp; rough weather recovery.&nbsp; I don't have actual collection depths for these three samples.
\_____________________\_
*Feb* {color:#0000ff}2016{color} &nbsp;
Repeat Dec flight.&nbsp; 1 LnG fired first, then 4 Archives on Makai.&nbsp; Samples taken at 8.7m, 12.7m, 13m, 27m, and 27m.

*Dec* {color:#0000ff}2016{color} &nbsp;
Depth testing with Honu in Makai.&nbsp; 5 archival cartridges.&nbsp; Fired at chl max (~14m), 50m, and 100m.&nbsp; 200m cartridge started, but vehicle cut ESP power before finished.&nbsp; 300m sample had carousel alignment issue and did not complete.&nbsp; 3 of 5 samples preserved.
\_____________________\_
*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; meet with R/V Shimada (CALCOFI ship).&nbsp; Difficulties with water in payload section and rough recovery.&nbsp; Three filters recovered (chl-max to compare to Shimada's, and two at 10m)

*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; CANON cruise and WF rendezvous.&nbsp; Alignment problem had us bypass (so we thought) cartridge #1.&nbsp; Four archives collected, two a smear from 40m to surface, two from 60m to surface.&nbsp; These are matched to ship samples Kevan collected.
\_____________________\_

Overall, we have 21 archival filters that correctly filtered and preserved samples; two LnG samples were collected (were both run through SPR on the vehicle?)
{panel}

h4. {color:#ff00cc}Makai flight w ESP-Koa and 60 Archive Cartridges{color}

*Dec 12 - 20, 2017*

We decided to generate 5 'blocks' of behavior (below) each testing a certain collection scheme, with replicates.&nbsp; Combined samples for Ed with samples for eDNA work.

Out of 60 cartridges, 15 are controls (9 pre-experiment + 6 post-experiment); 45 will be fired offshore.
The 45 field samples are divided into 5 blocks, each block containing 9 samples.
In each 9-sample block, firings are in triplicate bursts: 1, 2, 3 in one continuous burst; then 4, 5, 6; and then 7, 8, 9.

Scientists and engineers will jointly select appropriate sampling locations in consideration of oceanographic features as well as LRAUV operation safety.

Block 1 (Bathymetry alert due to deep sampling):
Mission files:
chlpeak_sampling_InAboveBelow.xml, in donut mode.
depth_sequence_sampling.xml
First, vehicle transits to M1-northeast: 36.760, \-122.012
Then, kick off mission, setting waypoint to M1. Vehicle will do an horizontal search for high chl between M1-northeast \[36.760, \-122.012\] and M1 \[36.750, \-122.022\]; set the hi-chl spot as the sampling location; run a cylinder around the sampling location
Run chlpeak_sampling_InAboveBelow.xml:
3 samples at vertical chl peak depth
Then, run depth_sequence_sampling.xml:
3 samples at 100m depth
3 samples at 250m depth
Total: 9 samples, \~15 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time).

Block 2 (Bathymetry alert due to deep sampling):
Mission file: smear_sampling.xml, in donut mode, on the first 3 samples.
Mission file: depth_sequence_sampling.xml, in donut mode, on the remaining 6 samples.
3 samples smearing between 5m and 100m depths
3 samples at 100m depth
3 samples at 5m depth
Total: 9 samples, \~14 hours (presuming 1hr filtration time + 0.5hr processing time for each sample)

Block 3:
Mission file: isotherm_sampling.xml, in donut mode.
Initial horizontal search for high chl in local area; set the hi-chl spot as the sampling location; run a cylinder around sampling location
3 samples at the temperature corresponding to the vertical chl peak.
3 samples at chlpeak temp - deltaT1
3 samples at chlpeak temp + deltaT2
Total: 9 samples, \~15 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time).

Block 4:
Mission file: chlpeak_sampling_InAboveBelow.xml.xml, in drift mode.
Initial horizontal search for high chl in local area; set the hi-chl spot as the sampling location; run a cylinder around sampling location
3 samples at chl peak depth
Vertical perturbation to reacquire chl peak
3 samples at chl peak depth
Vertical perturbation to reacquire chl peak
3 samples at chl peak depth
Total: 9 samples, \~16 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + initial horizontal hi-chl search and cylinder time + vertical perturbation time).

Block 5:
Mission file: depth_sequence_sampling.xml, in donut mode
Scientists determine a horizontal feature, and set a certain depth for sampling
3 samples at the set depth on one side of feature
3 samples at same depth in feature
3 samples at same depth on other side of feature
Total: 9 samples, \~16 hours (presuming 1hr filtration time + 0.5hr processing time for each sample + transit time)]]></property>
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<property name="body"><![CDATA[Present: Scott, Doug, Chris S., Jim, Addie, Brent
Absent: Wayne, Cheri, Kevin

h3.


h3. Machine Builds

* &nbsp;Allison replaced Mack o-rings with silicone (red ones); Roman doing dunk test in various reagents.
* Procedure when 'getting' any boards is to notifiy Dick Littlefield, who is the inventory keeper.&nbsp; Addie to let him know of the boards she borrowed from Wayne.

h3. MFB

* Addie has rec'd doctors instructions for bed rest until she has her baby, thus will not be returning to the lab after today.&nbsp; We will continue with the McLane visit using Cheri and Scott.
* Addie will change the stator and install Scott's taffy pull mixing tube on MFB1 so we may run PCR next week when Kendra comes to visit (Friday).
* We will order 9 regular 14-port stators
* First grill is called MFB1, MFB2 & MFB3 will be built with McLane.&nbsp; The MFB on the tombstone is called either 'MFBNeo' or 'the tombstone'.

h3. Software

* &nbsp;Garbage clean-up fix seems to have worked.&nbsp;
* Brent working on multiple config-file issues regarding linking MFB to a core
* Must make sure back-plane and grills are labeled, so&nbsp; config files stay linked to the appropriate grill
* We will visit check-out scripts with stops after the holidays

h3. DWSM


h6. +Sphere+

* Sphere dye tested (passed) and is returning from Wah Chang.&nbsp; Arrive tomorrow (Friday) or early next week.&nbsp;
* Much discussion of what we should pressure rate to.&nbsp; Depends on where we send it; 3000m will get to 90% of known vent sites.&nbsp; Port H. can test to 3700m.&nbsp; We will probably not go deeper than 2500m; Chris to talk to other ASTEP PI's.&nbsp; When we see what they want, we'll pass info to Doug, and test for that.

h6. +Elevator+

* &nbsp;Doug finished a 'walk-about' PDR with ship crew about what would work re: elevator design
* CDR for final elevator design; try to do by end of next week.
* Doug has calculated size envelope, weight balance, Center of Bouyancy, Center of Gravity.
* Leveling system should work fine to 8degree slope

*{+}DWSM{+}*
* &nbsp;All tubing is finished; just 4-5 days left for assembly.&nbsp; Progress slowed because of time put into elevator design.

h3. GUI Development

* &nbsp;Nothing

h3. Other Items:

* &nbsp;For January:&nbsp; must revisit puck order for both MOE and for 2 more cores coming along.&nbsp; Also HV puck design.&nbsp; Will talk to Mike Parker about this upon his return.
* Discussed attending JALA for Brent and Scott.&nbsp; Will decide Monday who wants/is willing to go.
* Much discussion about moving our deployment dates.&nbsp; If we can change current schedule, plan is as follows:
*** Dive 1:&nbsp; March 25--no core but elevator, DWSM, sphere
*** Dive 2:&nbsp; April 7--core in sphere, elevator, DWSM--run WCR
*** Dive 3:&nbsp; April 14--core in sphere, elevator, DWSM--minimal chemistry (SHA)
*** Dive 4:&nbsp; May 1-4--plug into MARS (date depends on what we can get that first week)
*** Dive 5:&nbsp; 1-3rd week of May \-\- pick up from MARS
*** JUNE 8-12--Flyer cruise (these dates may be moved a few days earlier, depending on DMO scheduling changes)
*** AUG 16-26--Flyer to Axial
*** Dive 6: Nov 4--plug into MARS, pickup in early 2010]]></property>
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<property name="body"><![CDATA[Present: Scott, Doug, Chris S., Jim, Addie, Brent
Absent: Wayne, Cheri, Kevin


h3.


h3. Machine Builds

* &nbsp;Allison replaced Mack o-rings with silicone (red ones); Roman doing dunk test in various reagents.
* Procedure when 'getting' any boards is to notifiy Dick Littlefield, who is the inventory keeper.&nbsp; Addie to let him know of the boards she borrowed from Wayne.

h3. MFB

* Addie has rec'd doctors instructions for bed rest until she has her baby, thus will not be returning to the lab after today.&nbsp; We will continue with the McLane visit using Cheri and Scott.
* Addie will change the stator and install Scott's taffy pull mixing tube on MFB1 so we may run PCR next week when Kendra comes to visit (Friday).
* We will order 9 regular 14-port stators
* First grill is called MFB1, MFB2 & MFB3 will be built with McLane.&nbsp; The MFB on the tombstone is called either 'MFBNeo' or 'the tombstone'.

h3. Software

* &nbsp;Garbage clean-up fix seems to have worked.&nbsp;
* Brent working on multiple config-file issues regarding linking MFB to a core
* Must make sure back-plane and grills are labeled, so&nbsp; config files stay linked to the appropriate grill
* We will visit check-out scripts with stops after the holidays

h3. DWSM


h6. +Sphere+

* Sphere dye tested (passed) and is returning from Wah Chang.&nbsp; Arrive tomorrow (Friday) or early next week.&nbsp;
* Much discussion of what we should pressure rate to.&nbsp; Depends on where we send it; 3000m will get to 90% of known vent sites.&nbsp; Port H. can test to 3700m.&nbsp; We will probably not go deeper than 2500m; Chris to talk to other ASTEP PI's.&nbsp; When we see what they want, we'll pass info to Doug, and test for that.

h6. +Elevator+

* &nbsp;Doug finished a 'walk-about' PDR with ship crew about what would work re: elevator design
* CDR for final elevator design; try to do by end of next week.
* Doug has calculated size envelope, weight balance, Center of Bouyancy, Center of Gravity.
* Leveling system should work fine to 8degree slope

*{+}DWSM{+}*
* &nbsp;All tubing is finished; just 4-5 days left for assembly.&nbsp; Progress slowed because of time put into elevator design.

h3. GUI Development

* &nbsp;Nothing

h3. Other Items:

* &nbsp;For January:&nbsp; must revisit puck order for both MOE and for 2 more cores coming along.&nbsp; Also HV puck design.&nbsp; Will talk to Mike Parker about this upon his return.
* Discussed attending JALA for Brent and Scott.&nbsp; Will decide Monday who wants/is willing to go.
* Much discussion about moving our deployment dates.&nbsp; If we can change current schedule, plan is as follows:
*** Dive 1:&nbsp; March 25--no core but elevator, DWSM, sphere
*** Dive 2:&nbsp; April 7--core in sphere, elevator, DWSM--run WCR
*** Dive 3:&nbsp; April 14--core in sphere, elevator, DWSM--minimal chemistry (SHA)
*** Dive 4:&nbsp; May 1-4--plug into MARS (date depends on what we can get that first week)
*** Dive 5:&nbsp; 1-3rd week of May \-\- pick up from MARS
*** JUNE 8-12--Flyer cruise (these dates may be moved a few days earlier, depending on DMO scheduling changes)
*** AUG 16-26--Flyer to Axial
*** Dive 6: Nov 4--plug into MARS, pickup in early 2010]]></property>
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<property name="body"><![CDATA[h2. Quotes

* Sphere casting [(Wah Chang)|^Wah Chang quote MBARI 60200 11-14 C5.pdf] \[1st piece arrived May 7, 2008\]
* Machining
** [Tapemation|^Tapemation quote MBARI 4K Hemi.doc]
** Hanard Machine (sent for quote 11-15-07 \--> [negative response])
** Sphere pictures are located in [http://mww.mbari.org/ProjectLibrary/ESP/DWSM/4K]%DWSM/4k%Sphere%Pictures]]></property>
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<property name="body"><![CDATA[h2. Quotes

* Sphere casting [(Wah Chang)|^Wah Chang quote MBARI 60200 11-14 C5.pdf] \[1st piece arrived May 7, 2008\]
* Machining
** [Tapemation|^Tapemation quote MBARI 4K Hemi.doc]
** Hanard Machine (sent for quote 11-15-07 \--> [negative response])
** Sphere pictures are located in [http://mww.mbari.org/ProjectLibrary/ESP/DWSM/4K%DWSM/4k%Sphere%Pictures]]]></property>
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<property name="body"><![CDATA[h2. Quotes

* Sphere casting [(Wah Chang)|^Wah Chang quote MBARI 60200 11-14 C5.pdf] \[1st piece arrived May 7, 2008\]
* Machining
** [Tapemation|^Tapemation quote MBARI 4K Hemi.doc]
** Hanard Machine (sent for quote 11-15-07 \--> [negative response])]]></property>
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<property name="body"><![CDATA[h2. Quotes

* Sphere casting [(Wah Chang)|^Wah Chang quote MBARI 60200 11-14 C5.pdf] \[1st piece arrived May 7, 2008\]
* Machining
** [Tapemation|^Tapemation quote MBARI 4K Hemi.doc]
** Hanard Machine (sent for quote 11-15-07 \--> [negative response])
** Sphere pictures are located in http://mww.mbari.org/ProjectLibrary/ESP/DWSM/4K DWSM/4k Sphere Pictures]]></property>
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<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.

June 26 - continues to run, but lost internet access due to an unknown networking error.

h3. {color:#ff00ff}So. California Deployment of ESP-Gordon / NEO{color}

Aug 30 \-\- Haul instrument and gear in trailer and MBARI van to deploy on OCSD R/V Nerissa.  Calm seas, hot weather, instrument in \~10:30am.  Gordon w/PCR, CTD, ISUS, cell-phone modem (T-Mobile).  Sewage diversion to begin Sep 11, 2012. Machine located at 33.59703 \-117.94623

Kevan collecting data here: [http://www.stanford.edu/~kevany/ESP/].

Sep 14-noticed CTD battery draining faster than expected because of optode.&nbsp; Also, ATV encoder in MFB&nbsp; kept returning 511, which is 2**9-1&nbsp; meaning all bits are stuck high--typical way they fail.&nbsp; Stopped PCR, continued SHA, but with dead CTD no contextual data to adaptive sample off of.&nbsp; Decision to flip for NEO on Sep 26.

Sep 26--recovered ESP-Gordon and swapped both batteries and ESP-Neo.&nbsp; Also changed CTD so now no optode (O2) measurments.&nbsp; One power cable fizzed away.&nbsp; Connector on pickle jar loose.&nbsp; But NEO now running well. Skipper gave deployment coordinates of 33 35.829 &nbsp; \-117 56.759.&nbsp; Xeos says&nbsp; 33.59702 \-117.94604.&nbsp; Water depth 18m.&nbsp; CTD/can depth=6.3m

h3. {color:#ff00ff}Fall CANON--Drifter with ESP-Moe / Moe{color}

WF leaves MBARI Sept 10.&nbsp; Moe with PCR, ISUS, CTD, PAR, and buoy has downward ADCP.&nbsp; Roman and Julie R. on ship.

Moe went into water Sep 11. First phase slated for 6pm.

Pulled Sep 17 (10:30am).&nbsp; E/M cable started flaking out either due to connector or bad ethernet extender.&nbsp; Decision to end mission unrelated to this. ]]></property>
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<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.

June 26 - continues to run, but lost internet access due to an unknown networking error.

h3. {color:#ff00ff}So. California Deployment of ESP-Gordon / NEO{color}

Aug 30 \-\- Haul instrument and gear in trailer and MBARI van to deploy on OCSD R/V Nerissa.  Calm seas, hot weather, instrument in \~10:30am.  Gordon w/PCR, CTD, ISUS, cell-phone modem (T-Mobile).  Sewage diversion to begin Sep 11, 2012. Machine located at 33.59703 \-117.94623.&nbsp; Divers from Orange County Sheriff's dept.


Kevan collecting data here: [http://www.stanford.edu/~kevany/ESP/].

Sep 14-noticed CTD battery draining faster than expected because of optode.&nbsp; Also, ATV encoder in MFB&nbsp; kept returning 511, which is 2**9-1&nbsp; meaning all bits are stuck high--typical way they fail.&nbsp; Stopped PCR, continued SHA, but with dead CTD no contextual data to adaptive sample off of.&nbsp; Decision to flip for NEO on Sep 26.

Sep 26--recovered ESP-Gordon and swapped both batteries and ESP-Neo.&nbsp; Also changed CTD so now no optode (O2) measurments.&nbsp; One power cable fizzed away.&nbsp; Connector on pickle jar loose.&nbsp; But NEO now running well. Skipper gave deployment coordinates of 33 35.829 &nbsp; \-117 56.759.&nbsp; Xeos says&nbsp; 33.59702 \-117.94604.&nbsp; Water depth 18m.&nbsp; CTD/can depth=6.3m.&nbsp; Divers from LBAoP--Eric Castillo and Steve Lang.


Oct 16--Recovered ESP-Neo.&nbsp; Divers from LBAoP--Steve Lang and Veronica Anderson.


h3. {color:#ff00ff}Fall CANON--Drifter with ESP-Moe / Moe{color}

WF leaves MBARI Sept 10.&nbsp; Moe with PCR, ISUS, CTD, PAR, and buoy has downward ADCP.&nbsp; Roman and Julie R. on ship.

Moe went into water Sep 11. First phase slated for 6pm.

Pulled Sep 17 (10:30am).&nbsp; E/M cable started flaking out either due to connector or bad ethernet extender.&nbsp; Decision to end mission unrelated to this. ]]></property>
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<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.

June 26 - continues to run, but lost internet access due to an unknown networking error.

h3. {color:#ff00ff}So. California Deployment of ESP-Gordon / NEO{color}

Aug 30 \-\- Haul instrument and gear in trailer and MBARI van to deploy on OCSD R/V Nerissa.  Calm seas, hot weather, instrument in \~10:30am.  Gordon w/PCR, CTD, ISUS, cell-phone modem (T-Mobile).  Sewage diversion to begin Sep 11, 2012. Machine located at 33.59703 \-117.94623.&nbsp; Divers from Orange County Sheriff's dept.

Kevan collecting data here: [http://www.stanford.edu/~kevany/ESP/].

Sep 14-noticed CTD battery draining faster than expected because of optode.&nbsp; Also, ATV encoder in MFB&nbsp; kept returning 511, which is 2**9-1&nbsp; meaning all bits are stuck high--typical way they fail.&nbsp; Stopped PCR, continued SHA, but with dead CTD no contextual data to adaptive sample off of.&nbsp; Decision to flip for NEO on Sep 26.

Sep 26-\--recovered ESP-Gordon and swapped both batteries and ESP-Neo.&nbsp; Also changed CTD so now no optode (O2) measurments.&nbsp; One power cable fizzed away.&nbsp; Connector on pickle jar loose.&nbsp; But NEO now running well. Skipper gave deployment coordinates of 33 35.829 &nbsp; \-117 56.759.&nbsp; Xeos says&nbsp; 33.59702 \-117.94604.&nbsp; Water depth 18m.&nbsp; CTD/can depth=6.3m.&nbsp; Divers from LBAoP-\-Eric Castillo and Steve Lang.

Oct 16\--\-Recovered ESP-Neo.&nbsp; Divers from LBAoP-\-Steve Lang and Veronica Anderson.

h3. {color:#ff00ff}Fall CANON--Drifter with ESP-Moe / Moe{color}

WF leaves MBARI Sept 10.&nbsp; Moe with PCR, ISUS, CTD, PAR, and buoy has downward ADCP.&nbsp; Roman and Julie R. on ship.

Moe went into water Sep 11. First phase slated for 6pm.

Pulled Sep 17 (10:30am).&nbsp; E/M cable started flaking out either due to connector or bad ethernet extender.&nbsp; Decision to end mission unrelated to this. ]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| | G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| 1 \\ | Ambient Flush Reservoir \\ | * Mixtures, chemicals?
* Volume (s)
* Material compatibility
* Dilution with SW?
* Flush fluids as well? | | \\ | 1 |
| 2 | Intake point and Screen \\ | * Single intake?
* CU screens?
* Location on LRAUV
* Min bore size? | | | 2 |
| 3 | | | | | |
| 4 | Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * Number of ports (intakes and ambient storage)?
* 3-way valve
* Min bore size?
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| 5 | Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi
* Min bore size?
* Non-corroding
* Fail closed
* Wattage? Power budget?
* Small scale, Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| 6 | Cartridge Selection valves \\ | * Chemical suitable
* 500 psi
* Min bore size?
* low power
* flush free | * Ladder/Looper options
* 2 position spool valves
* Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| 7 | Cartridge Return Array \\ | | * check valve
* part of Selection valve
*  | * LeeCo
* Parker | 4 |
| 8 | Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
* Testing process, procedure
* Vibration testing? | * Dibafit
* Upchurch
* LeeCo | 1 |
| 9 | Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| 10 | Filter selection valving \\
(transition from sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | * Rotary valve, reagent select, part of filter holder
*  | | 4 |
| 11 | Cartridge Seals \\ | Connection between spool valves, cartridges to cartridge\\ | | | 2 |
| 12 | \\ | | | | |
| 13 | \\ | \\ | \\ | | |
| 14 | Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| 15 | Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| 16 | Filter Evacuate \\ | * Need to remove seawater <5% of lysis volume.
* In G2, remaining seawater needs to be <100uL
* For 1mL lysis volume, <50uL, or <1 drop.
** Test numbers: Dry filter \+holder, 9.91g
** wet filter (filter holder dry) 9.95g (40 uL)
** no change if vacuumed, no change w/ singe 10ml blow thru
** after 3X 10mL blow thru, 9.92g (10 uL)
** filter appeared to be mostly dry | * Air pressure evac (G2 method)
* Vacuum assist below filter?
* Filter holder is piston assembly, w/ small dead volumes
* Displacement with other fluid? | | 4 |
| 17 | Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| 18 | DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| 19 | Direct Capture \\ | | | | |
| 20 | Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| 21 | Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| 22 | | | | | |
| 23 | Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| 24 | Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| 25 | Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| 26 | Cartridge Actuators \\ | | | | 4 |
| 27 | \\ | \\ | \\ | \\ | |
| 28 | Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| 29 | Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| 30 | | | | | |
| 31 | TRANSFER TO AM | | | | |
| 32 | Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| 33 | AM Selector Injection Loop \\ | | | | 4 \\ |
| 34 | Clean Injection Loop \\ | | | | 4 \\ |
| 35 | Rotor Pass-Thru \\ | | | | 2 |
| 36 | LRAUV Platform Interface \\ | | | | 2 \\ |
| 37 | LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | See model \\
G3LRAUVHousing.sldasm \\ | 2 \\ |
| 38 | | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[{gliffy:name=Mtg Rev|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| | G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| 1 \\ | Ambient Flush Reservoir \\ | * Mixtures, chemicals?
* Volume (s)
* Material compatibility
* Dilution with SW?
* Flush fluids as well? | | \\ | 1 |
| 2 | Intake point and Screen \\ | * Single intake?
* CU screens?
* Location on LRAUV
* Min bore size? | | | 2 |
| 3 | | | | | |
| 4 | Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * Number of ports (intakes and ambient storage)?
* 3-way valve
* Min bore size?
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| 5 | Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi
* Min bore size?
* Non-corroding
* Fail closed
* Wattage? Power budget?
* Small scale, Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| 6 | Cartridge Selection valves \\ | * Chemical suitable
* 500 psi
* Min bore size?
* low power
* flush free | * Ladder/Looper options
* 2 position spool valves
* Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| 7 | Cartridge Return Array \\ | | * check valve
* part of Selection valve
*  | * LeeCo
* Parker | 4 |
| 8 | Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
* Testing process, procedure
* Vibration testing? | * Dibafit
* Upchurch
* LeeCo | 1 |
| 9 | Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| 10 | Filter selection valving \\
(transition from sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | * Rotary valve, reagent select, part of filter holder
*  | | 4 |
| 11 | Cartridge Seals \\ | Connection between spool valves, cartridges to cartridge\\ | | | 2 |
| 12 | \\ | | | | |
| 13 | \\ | \\ | \\ | | |
| 14 | Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| 15 | Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| 16 | Filter Evacuate \\ | * Need to remove seawater <5% of lysis volume.
* In G2, remaining seawater needs to be <100uL
* For 1mL lysis volume, <50uL, or <1 drop.
** Test numbers: Dry filter \+holder, 9.91g
** wet filter (filter holder dry) 9.95g (40 uL)
** no change if vacuumed, no change w/ singe 10ml blow thru
** after 3X 10mL blow thru, 9.92g (10 uL)
** filter appeared to be mostly dry | * Air pressure evac (G2 method)
* Vacuum assist below filter?
* Filter holder is piston assembly, w/ small dead volumes
* Displacement with other fluid? | | 4 |
| 17 | Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| 18 | DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| 19 | Direct Capture \\ | | | | |
| 20 | Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| 21 | Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| 22 | | | | | |
| 23 | Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| 24 | Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| 25 | Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| 26 | Cartridge Actuators \\ | | | | 4 |
| 27 | \\ | \\ | \\ | \\ | |
| 28 | Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| 29 | Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| 30 | | | | | |
| 31 | TRANSFER TO AM | | | | |
| 32 | Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| 33 | AM Selector Injection Loop \\ | | | | 4 \\ |
| 34 | Clean Injection Loop \\ | | | | 4 \\ |
| 35 | Rotor Pass-Thru \\ | | | | 2 |
| 36 | LRAUV Platform Interface \\ | | | | 2 \\ |
| 37 | LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | See model \\
G3LRAUVHousing.sldasm \\ | 2 \\ |
| 38 | | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[
{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| | G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| 1 \\ | Ambient Flush Reservoir \\ | * Mixtures, chemicals?
* Volume (s)
* Material compatibility
* Dilution with SW?
* Flush fluids as well? | | \\ | 1 |
| 2 | Intake point and Screen \\ | * Single intake?
* CU screens?
* Location on LRAUV
* Min bore size? | | | 2 |
| 3 | | | | | |
| 4 | Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * Number of ports (intakes and ambient storage)?
* 3-way valve
* Min bore size?
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| 5 | Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi
* Min bore size?
* Non-corroding
* Fail closed
* Wattage? Power budget?
* Small scale, Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| 6 | Cartridge Selection valves \\ | * Chemical suitable
* 500 psi
* Min bore size?
* low power
* flush free | * Ladder/Looper options
* 2 position spool valves
* Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| 7 | Cartridge Return Array \\ | | * check valve
* part of Selection valve
*  | * LeeCo
* Parker | 4 |
| 8 | Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
* Testing process, procedure
* Vibration testing? | * Dibafit
* Upchurch
* LeeCo | 1 |
| 9 | Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| 10 | Filter selection valving \\
(transition from sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | * Rotary valve, reagent select, part of filter holder
*  | | 4 |
| 11 | Cartridge Seals \\ | Connection between spool valves, cartridges to cartridge\\ | | | 2 |
| 12 | \\ | | | | |
| 13 | \\ | \\ | \\ | | |
| 14 | Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| 15 | Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| 16 | Filter Evacuate \\ | * Need to remove seawater <5% of lysis volume.
* In G2, remaining seawater needs to be <100uL
* For 1mL lysis volume, <50uL, or <1 drop.
** Test numbers: Dry filter \+holder, 9.91g
** wet filter (filter holder dry) 9.95g (40 uL)
** no change if vacuumed, no change w/ singe 10ml blow thru
** after 3X 10mL blow thru, 9.92g (10 uL)
** filter appeared to be mostly dry | * Air pressure evac (G2 method)
* Vacuum assist below filter?
* Filter holder is piston assembly, w/ small dead volumes
* Displacement with other fluid? | | 4 |
| 17 | Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| 18 | DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| 19 | Direct Capture \\ | | | | |
| 20 | Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| 21 | Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| 22 | | | | | |
| 23 | Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| 24 | Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| 25 | Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| 26 | Cartridge Actuators \\ | | | | 4 |
| 27 | \\ | \\ | \\ | \\ | |
| 28 | Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| 29 | Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| 30 | | | | | |
| 31 | TRANSFER TO AM | | | | |
| 32 | Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| 33 | AM Selector Injection Loop \\ | | | | 4 \\ |
| 34 | Clean Injection Loop \\ | | | | 4 \\ |
| 35 | Rotor Pass-Thru \\ | | | | 2 |
| 36 | LRAUV Platform Interface \\ | | | | 2 \\ |
| 37 | LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | See model \\
G3LRAUVHousing.sldasm \\ | 2 \\ |
| 38 | | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| | G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| 1 \\ | Ambient Flush Reservoir \\ | * Mixtures, chemicals?
* Volume (s)
* Material compatibility
* Dilution with SW?
* Flush fluids as well? | | \\ | 1 |
| 2 | Intake point and Screen \\ | * Single intake?
* CU screens?
* Location on LRAUV
* Min bore size? | | | 2 |
| 3 | | | | | |
| 4 | Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * Number of ports (intakes and ambient storage)?
* 3-way valve
* Min bore size?
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| 5 | Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi
* Min bore size?
* Non-corroding
* Fail closed
* Wattage? Power budget?
* Small scale, Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| 6 | Cartridge Selection valves \\ | * Chemical suitable
* 500 psi
* Min bore size?
* low power
* flush free | * Ladder/Looper options
* 2 position spool valves
* Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| 7 | Cartridge Return Array \\ | | * check valve
* part of Selection valve
*  | * LeeCo
* Parker | 4 |
| 8 | Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
* Testing process, procedure
* Vibration testing? | * Dibafit
* Upchurch
* LeeCo | 1 |
| 9 | Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| 10 | Filter selection valving \\
(transition from sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | * Rotary valve, reagent select, part of filter holder
*  | | 4 |
| 11 | Cartridge Seals \\ | Connection between spool valves, cartridges to cartridge\\ | | | 2 |
| 12 | \\ | | | | |
| 13 | \\ | \\ | \\ | | |
| 14 | Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| 15 | Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| 16 | Filter Evacuate \\ | * Need to remove seawater <5% of lysis volume.
* In G2, remaining seawater needs to be <100uL
* For 1mL lysis volume, <50uL, or <1 drop.
** Test numbers: Dry filter \+holder, 9.91g
** wet filter (filter holder dry) 9.95g (40 uL)
** no change if vacuumed, no change w/ singe 10ml blow thru
** after 3X 10mL blow thru, 9.92g (10 uL)
** filter appeared to be mostly dry | * Air pressure evac (G2 method)
* Vacuum assist below filter?
* Filter holder is piston assembly, w/ small dead volumes
* Displacement with other fluid? | | 4 |
| 17 | Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| 18 | DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| 19 | Direct Capture \\ | | | | |
| 20 | Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| 21 | Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| 22 | | | | | |
| 23 | Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| 24 | Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| 25 | Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| 26 | Cartridge Actuators \\ | | | | 4 |
| 27 | \\ | \\ | \\ | \\ | |
| 28 | Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| 29 | Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| 30 | | | | | |
| 31 | TRANSFER TO AM | | | | |
| 32 | Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| 33 | AM Selector Injection Loop \\ | | | | 4 \\ |
| 34 | Clean Injection Loop \\ | | | | 4 \\ |
| 35 | Rotor Pass-Thru \\ | | | | 2 |
| 36 | LRAUV Platform Interface \\ | | | | 2 \\ |
| 37 | LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | See model \\
G3LRAUVHousing.sldasm \\ | 2 \\ |
| 38 | | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.
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<property name="body"><![CDATA[
{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| | G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| 1 \\ | Ambient Flush Reservoir \\ | * Mixtures, chemicals?
* Volume (s)
* Material compatibility
* Dilution with SW?
* Flush fluids as well? | | \\ | 1 |
| 2 | Intake point and Screen \\ | * Single intake?
* CU screens?
* Location on LRAUV
* Min bore size? | | | 2 |
| 3 | | | | | |
| 4 | Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * Number of ports (intakes and ambient storage)?
* 3-way valve
* Min bore size?
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| 5 | Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi
* Min bore size?
* Non-corroding
* Fail closed
* Wattage? Power budget?
* Small scale, Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| 6 | Cartridge Selection valves \\ | * Chemical suitable
* 500 psi
* Min bore size?
* low power
* flush free | * Ladder/Looper options
* 2 position spool valves
* Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| 7 | Cartridge Return Array \\ | | * check valve
* part of Selection valve
*  | * LeeCo
* Parker | 4 |
| 8 | Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
* Testing process, procedure
* Vibration testing? | * Dibafit
* Upchurch
* LeeCo | 1 |
| 9 | Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| 10 | Filter selection valving \\
(transition from sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | * Rotary valve, reagent select, part of filter holder
*  | | 4 |
| 11 | Cartridge Seals \\ | Connection between spool valves, cartridges to cartridge\\ | | | 2 |
| 12 | \\ | | | | |
| 13 | \\ | \\ | \\ | | |
| 14 | Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| 15 | Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| 16 | Filter Evacuate \\ | * Need to remove seawater <5% of lysis volume.
* In G2, remaining seawater needs to be <100uL
* For 1mL lysis volume, <50uL, or <1 drop.
** Test numbers: Dry filter \+holder, 9.91g
** wet filter (filter holder dry) 9.95g (40 uL)
** no change if vacuumed, no change w/ singe 10ml blow thru
** after 3X 10mL blow thru, 9.92g (10 uL)
** filter appeared to be mostly dry | * Air pressure evac (G2 method)
* Vacuum assist below filter?
* Filter holder is piston assembly, w/ small dead volumes
* Displacement with other fluid? | | 4 |
| 17 | Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| 18 | DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| 19 | Direct Capture \\ | | | | |
| 20 | Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| 21 | Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| 22 | | | | | |
| 23 | Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| 24 | Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| 25 | Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| 26 | Cartridge Actuators \\ | | | | 4 |
| 27 | \\ | \\ | \\ | \\ | |
| 28 | Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| 29 | Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| 30 | | | | | |
| 31 | TRANSFER TO AM | | | | |
| 32 | Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| 33 | AM Selector Injection Loop \\ | | | | 4 \\ |
| 34 | Clean Injection Loop \\ | | | | 4 \\ |
| 35 | Rotor Pass-Thru \\ | | | | 2 |
| 36 | LRAUV Platform Interface \\ | | | | 2 \\ |
| 37 | LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | See model \\
G3LRAUVHousing.sldasm \\ | 2 \\ |
| 38 | | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.
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<property name="body"><![CDATA[
{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| | G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| 1 \\ | Ambient Flush Reservoir \\ | * Mixtures, chemicals?
* Volume (s)
* Material compatibility
* Dilution with SW?
* Flush fluids as well? | | \\ | 1 |
| 2 | Intake point and Screen \\ | * Single intake?
* CU screens?
* Location on LRAUV
* Min bore size? | | | 2 |
| 3 | | | | | |
| 4 | Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * Number of ports (intakes and ambient storage)?
* 3-way valve
* Min bore size?
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| 5 | Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi
* Min bore size?
* Non-corroding
* Fail closed
* Wattage? Power budget?
* Small scale, Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| 6 | Cartridge Selection valves \\ | * Chemical suitable
* 500 psi
* Min bore size?
* low power
* flush free | * Ladder/Looper options
* 2 position spool valves
* Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| 7 | Cartridge Return Array \\ | | * check valve
* part of Selection valve
*  | * LeeCo
* Parker | 4 |
| 8 | Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
* Testing process, procedure
* Vibration testing? | * Dibafit
* Upchurch
* LeeCo | 1 |
| 9 | Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| 10 | Filter selection valving \\
(transition from sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | * Rotary valve, reagent select, part of filter holder
*  | | 4 |
| 11 | Cartridge Seals \\ | Connection between spool valves, cartridges to cartridge\\ | | | 2 |
| 12 | \\ | | | | |
| 13 | \\ | \\ | \\ | | |
| 14 | Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| 15 | Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| 16 | Filter Evacuate \\ | * Need to remove seawater <5% of lysis volume.
* In G2, remaining seawater needs to be <100uL
* For 1mL lysis volume, <50uL, or <1 drop.
** Test numbers: Dry filter \+holder, 9.91g
** wet filter (filter holder dry) 9.95g (40 uL)
** no change if vacuumed, no change w/ singe 10ml blow thru
** after 3X 10mL blow thru, 9.92g (10 uL)
** filter appeared to be mostly dry | * Air pressure evac (G2 method)
* Vacuum assist below filter?
* Filter holder is piston assembly, w/ small dead volumes
* Displacement with other fluid? | | 4 |
| 17 | Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| 18 | DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| 19 | Direct Capture \\ | | | | |
| 20 | Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| 21 | Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| 22 | | | | | |
| 23 | Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| 24 | Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| 25 | Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| 26 | Cartridge Actuators \\ | | | | 4 |
| 27 | \\ | \\ | \\ | \\ | |
| 28 | Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| 29 | Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| 30 | | | | | |
| 31 | TRANSFER TO AM | | | | |
| 32 | Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| 33 | AM Selector Injection Loop \\ | | | | 4 \\ |
| 34 | Clean Injection Loop \\ | | | | 4 \\ |
| 35 | Rotor Pass-Thru \\ | | | | 2 |
| 36 | LRAUV Platform Interface \\ | | | | 2 \\ |
| 37 | LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | See model \\
G3LRAUVHousing.sldasm \\ | 2 \\ |
| 38 | | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.

{gliffy:name=Mtg Version|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}]]></property>
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<property name="body"><![CDATA[h2. Opening the ESP project in an IDEA

h3. Eclipse
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# cd to the directory you checked it out to
# In a terminal run: {code}mvn eclipse:eclipse{code}
# In eclipse do _File->import_
#* Select _existing project from workspace_


h3. IntelliJ IDEA
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# cd to the directory you checked it out to
# In a terminal run: {code}mvn idea:idea{code}
# Do _File->Open Project_

h3. JBuilder
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# In Jbuilder do _File->import_
# Select _existing maven project from workspace_

h3. Netbeans
# [Check out the esp/trunk from SVN|http://oceana/projects/esp/source-repository.html]
# Install the Maven plug-in in Netbeans
## Select _Tools-Plugins_
## In the dialog that appears, select the _New Plugins_ tab
## Check the box next to *Maven*
## Press the install button
# Do _File->Open Project_
# Select the project (Netbeans will open all the child projects too)
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application
{panel}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation. Done in three stages
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
{jiraissues:https://oceana.mbari.org/jira/sr/jira.issueviews:searchrequest-xml/temp/SearchRequest.xml?&pid=10050&status=1&status=3&status=4&component=10082&sorter/field=issuekey&sorter/order=DESC&sorter/field=priority&sorter/order=DESC&tempMax=1000|anonymous=true}
{panel}
h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]


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<property name="body"><![CDATA[h2. For the developers

# [Getting the source|http://oceana/projects/esp/source-repository.html]
# [Opening in an IDE]
# [Image Processing]]]></property>
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<property name="body"><![CDATA[{section}
{column}
As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.
{column}
{column}
&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
{column}
{section}


So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Data Import

{mockup:Data_Import|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Data Import

{mockup:Data_Import|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[This page lists some terminology and their definitions and context as they were used in the design work of the GUI application.  This is to ensure that when discussions are occurring, we are all talking about the same thing.

# +*Mission*+ This is a logical span of time in which an ESP instrument is operating which has some start and end time.  It is usually associated with a the deployment and recovery of an ESP.
# +*Protocol Run*+ Also just called _protocol_. A sequence of steps (think recipe) that the ESP goes through to achieve a specific goal. Each protocol run will have one puck and filter.
# +*Phase*+ Is a sequence of protocol runs that.  Examples of phases are HAB, BAC, LARV.  The concept of a phase is important as a mission script is defined using phases.  Phases can contain protocol sequence that will take more than one sample of water. i.e. The relationship between phase and sample is one-to-many.
# +*Deployment*+ Is used synonymously with *Mission*.
# +*Mission Script*+ An ASCII file that contains Ruby commands that tell the ESP what actions to take at what times.
# +*Puck*+ Metal ring that holds filter paper which is used to capture and process organisms.
# +*Filter*+ Special paper that is printed with various materials to help in detection of organisms. Not all filters have probes on them (for example, WCR has not probes as it just archives the organisms).
# +*Probe*+
# +*SH*+ Acronym for Sandwich Hybridization
# +*GAL File*+ File that is produced by the filter printer and contains the locations in X,Y coordinates and what probes are at those X,Y coordinates.
# +*Standard Curve*+ A curve that maps intensity to density of organisms.  You use it to take the intensity of an image and calculate the density of organisms in the sample.
# +*Sample Volume*+ A volume of water that is brought into the instrument that contains the organisms which the instrument is attempting to identify.
# +*Consumable*+ Is any resources on the instrument that can be consumed.  Examples are:
## Power
## Reagants
## Capacities like waste (there are 2)
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<property name="body"><![CDATA[h3. Minutes
{section}
{column:width=60%}
# Phases: HAB, BAC, LARV
# Phases run protocols
# Phase is a series of operations (could be one protocol, but more likely more).  Can be one puck, but more likely more.
# Phase is a standard set of operations
# Each protocol needs a puck (with filter)
# Filter may or may not have probes, whole cell has no probes, just brings home sample
# All pucks have serial numbers.
# pucks outer diameter is the same.
# there are different pucks for different
# SH = standard hybridization, detect molecules of interest. Heat it up and liquify.  Filter and then apply to SH2.  SH1 pucks can be used lysate.
# Why do we want to keep track of serial numbers on pucks
# Once puck is closed, not sure what is in there.
# Serial numbers help keep track of what they intend to use it for after build.
# Some have physical specimen and they need to figure out which puck has the specimen
# After filteration, put on another filter, then more chemistry, then image.
# Final PUCK is WCR (whole cell archival) is then sample is then preserved and brought home for shore side analysis
# Associated with probes is spot map (array map) ".Gal File" (what probe in what X,Y location).  Often listed as "Spot 23" then lookup with tell you X,Y
# Image is analyzed and you get intensities.
# Device can do "auto exposure" to figure out where it needs to be to get image in linear range of CCD chip.
# Also ask for constant exposure (do more than one constant exposure).
# Use standard curves and control spots on map.
# Standard curve is number of bugs/intensity
# Run exposure that you have standard curve for and then get intensity which then you lookup on the spot map.
# Low res images come across the wire (high res is 1MB).
# Phases can change the protocols (should we force users to use unique names- Chris thinks this would be good)
# Array map evolves.
# Protocols use same reagants, same amount 
# Phase-protocol combination (Phase tells you what the amounts are in the different protocols)
# Volumes filtered varies (tell it "Collect a liter", instrument decides how much until to filter until clogged)
# Print info comes from "gal file".  Old print is excel file.
# Some filters are thrown away, some are archived.
# Comments also need to be captured.
# Events are "when we sample"
# User specifies start of phase
## Then delay (7 minutes let's say), then sample is taken (that is the actual "start").  The rest of the protocols depend on the environmental characteristics.
# There will be maximum time for each phase (can be shorter, never longer).
# Instrument capacities:
## Pucks: 
## Reagants: 20
## Waste: fixed in current machine
# Configuration file tells what reagents are at what valve.
# There is a waste 1 and waste 2 (NOTE this is dependent on the reagent. specify which waste reagent goes to)
# Power budget.
# Instrument run
## Take series of protocol, to build phases
## write high level script
## derive max volumes.
# Number of pucks is usual limitation
# sometimes waste can be limiter.
{column}
{column:width=40%}
{panel:title=Attendees}
# Chris Scholin
# Rich Schramm
# Brian Schlining
# Karen Salamy
# Kevin Gomes
{panel}
{panel:title=Outstanding Questions}
# Does the delay (7 minutes) only happen at the beginning of each phase or each protocol?
# Is max duration at the phase level or protocol level?
{panel}
{column}
{section}

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<property name="body"><![CDATA[h3. Minutes from Mock Mission Planning Meeting


h5. Questions

# How are volumes for duplicate phases handled?
{noformat}
# Sample Volumes for Assay Types
$habVol=1000
$larvVol=900
$larvVol=700
$daVol=30

startTube 2
# require '08feb'


startAt "14:44:34 03/12/2008"

initialPurge
hab
napUntil "10:05:13 03/13/2008"

larv
napUntil "05:50:00 03/14/2008"

initialPurge
larv
napUntil "17:45:00 03/14/2008"

da
shutdown
{noformat}
# Script gets generated but not in sync with timing of simulator/instrument, how to best synch:
{noformat}
CH.stop
I2C::MsgErr in sampler -- I2C::Servo::OffCmd Not yet modeled
I2C::MsgErr in storage -- I2C::Servo::OffCmd Not yet modeled
I2C::MsgErr in sampler -- I2C::Servo::ConfigureCmd Not yet modeled
I2C::MsgErr in storage -- I2C::Servo::ConfigureCmd Not yet modeled
CH.configure CHconfig
PH.stop
PH.configure PHconfig
Posix::Error in quick -- /dev/ctd not a character device
Starting with tube #2
delayUntil "06:15:00.00 PDT 13-Mar-08"
@06:15:00.00PDT13-Mar-08 <poll> CTD.startLogging
@06:15:00.00 <quick> Initial Intake Purge
@06:16:30.00 ==> hab 1000ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@09:46:30.00 Disinfect Intake
@09:48:30.00 Shutdown
delayUntil "13:50:00.00"
@12:15:00.00 <poll> CTD.update
@13:50:00.00 <quick> ==> bac 900ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@17:20:00.00 Disinfect Intake
@17:22:00.00 Shutdown
delayUntil "01:25:00.00 PDT 14-Mar-08"
@18:15:00.00 <poll> CTD.update
@00:15:00.00PDT14-Mar-08 CTD.update
@01:25:00.00 <quick> Initial Intake Purge
@01:26:30.00 ==> larv 900ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@04:56:30.00 Disinfect Intake
@04:58:30.00 Shutdown
delayUntil "11:20:00.00"
@06:15:00.00 <poll> CTD.update
@11:20:00.00 <quick> Initial Intake Purge
@11:21:30.00 ==> da 1000ml, :image=>[:hires, 15, :default, 4, :midres, :auto]
@12:15:00.00 <poll> CTD.update
@14:21:30.00 <quick> Disinfect Intake
@14:23:30.00 Shutdown
delayUntil "20:30:00.00"
@18:15:00.00 <poll> CTD.update
@20:30:00.00 <quick> Initial Intake Purge
@20:31:30.00 ==> hab 1000ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@00:01:30.00PDT15-Mar-08 ==> da 1000ml, :image=>[:hires, 15, :default, 4, :midres, :auto]
@00:15:00.00 <poll> CTD.update
@02:01:30.00 <quick> Disinfect Intake
@02:03:30.00 Shutdown
gui_test.rb Assays Completed. CTD logging continues ... 
delayUntil "00:13:07.00"
Schedule::Error in quick -- Delay::RunEvent for @00:13:07.00 PDT 15-Mar-08 is in the past
Waiting to Resume from Checkpoint "gui_test.rb Assays Completed. CTD logging continues ... "
@06:15:00.00 <poll> CTD.update
@12:15:00.00 CTD.update
@18:15:00.00 CTD.update
@00:15:00.00PDT16-Mar-08 CTD.update
{noformat}
{panel:title=New Requests}
# Have capability to add comments to phases that show up in script. Maybe go out in log too. Also add header comments. (global too).
# Modify protocol so it doesn't kill between phases (want capability to call out alternate purge).
# Always odd things (give it ruby and time to run and it puts it in script).
# Phases should be different colors
# BUG: If delete last phase, can't add one at end.
# Need to specify a way just to sequence things, not deterministic time. Or say, I just want to wait 15 minutes after it finishes.
# Have way to call out initial purge instead of upper/lowercase
{panel}
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering member to try to determine what the GUI needs to do.  The following requirements were gathered as part of that process:

h3. Requirements
{section}
{column:width=60%}
||Number||Requirement||Associated View||
|1|User can define missions by specifying phases|Planning|
|2|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|Be able to add non-phase/protocol events (user defined) to the calendar anywhere|Operation|
|5|Be able to set mission start end times that are not associated with a phase/protocol|Planning|
|6|Be able to specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User shall be able to add comments to a phase that will be generated in the script|Planning|
|8|User shall be able to view images associated with phases|Operation|
|9|User shall be able to browse the .GAL file along with image and filter paper information|Operation|
|10|User should be able to browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Operation|
|11|User should be able to browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Operation|
|12|User should be able to associate external files with events (excel spreadsheet, documents, etc.)|Planning,Operation|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|Operation|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users should have a form to add/delete/edit protocol runs and phases|Planning|
|16|Users should have a form to add/delete/edit consumables|Planning|
|17|In application users should have sample volume listed with protocol run|Planning|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should somehow be shown|Operation|
|19|Tide and phase information should be available during planning|Planning,Operation|
|20|Application should allow for details of flushes to be seen/accounted for|Operation|
|21|Users should be able to schedule Kills (end purges) or disable kills|Planning|
|22|Users should be able to define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to visualize the current state of the instrument|Operation,State|
|24|Users should be able to scroll back in time and visualize instrument state at the various points in time|State|
{column}
{column:width=40%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
{panel}
{panel:title=Supporting Docs}
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[# Do we need to track the serial numbers of the pucks in the application?
# If we print barcodes on filters, do we want to track in the application?
]]></property>
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<property name="body"><![CDATA[h2. For the developers

# [Getting the source|http://oceana/projects/esp/source-repository.html]
# [Opening in an IDE]
# [Scholin email - Things to track\- 07-Sep-2007|^ESPGUIDMthingstotrackextractfromlog.htm]
# [Image Processing]]]></property>
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<property name="body"><![CDATA[{section}
{column}
As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.
{column}
{column}
&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
{column}
{section}


So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Data Import

{mockup:Data_Import|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[{section}
{column}
As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.
{column}
{column}
&nbsp; !Logical Deployment Diagram.jpg!
{column}
{section}


So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Data Import

{mockup:Data_Import|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:
{section}
{column:width=60%}
{panel:title=Things to note}
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.
{panel}
{column}
{column}
&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
{column}
{section}


So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Data Import

{mockup:Data_Import|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[{section}
{column:width=60%}
As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.
{column}
{column}
&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
{column}
{section}


So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Data Import

{mockup:Data_Import|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[h3. PDR Meeting Notes (June 6, 2007)

# Attendees
## Rich Schramm
## Kevin Gomes
## Chris Scholin
## Doug Pargett
## Scott McLean
## Jim Birch
# Presentation
## [Powerpoint Slides (ppt)|ESPAPP:ProjectPresentations^PDR.ppt|Power Point Slides PDR]
# Demo Mockup
# [WBS and Costs (xls)|ESPAPP:ProjectPresentations^PDR.xls|WBS Spreadsheet]]]></property>
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<property name="body"><![CDATA[h3. PDR Meeting Notes (June 6, 2007)
{section}
{column:width=60%}
# Attendees
## Rich Schramm
## Kevin Gomes
## Chris Scholin
## Doug Pargett
## Scott McLean
## Jim Birch
{column}
{column:width=40%}
{panel:title=Documents}
# [Powerpoint Slides (ppt)|ESPAPP:ProjectPresentations^PDR.ppt|Power Point Slides PDR]
# Demo Mockup
# [WBS and Costs (xls)|ESPAPP:ProjectPresentations^PDR.xls|WBS Spreadsheet]
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering member to try to determine what the GUI needs to do.  The following requirements were gathered as part of that process:

{section}
{column:width=60%}
h3. Requirements
# User can define missions by specifying phases. (Operation View)
# User can specify and adjust phase start times. (Operation View)
# User can also specify a time to wait between events instead of a specific start time. (Operation View)
# Be able to add non-phase/protocol events (user defined) to the calendar anywhere. (Operation View)
# Be able to set mission start end times that are not associated with a phase/protocol. (Operation View)
# Be able to specify comments associated with missions that are printed at the top of the mission script. (Operation View)
# User shall be able to add comments to a phase that will be generated in the script. (Operation View)
# User shall be able to view images associated with phases. (Operation/Data Analysis View)
# User shall be able to browse the .GAL file along with image and filter paper information. (Operation/Data Analysis View)
# User should be able to browse image, click on intensity and application applies .GAL/Map with standard curves to give density. (Data Analysis)
# User should be able to browse the low-res images that come over the telemetry until full size image is offloaded after recovery. (Operation/Data Analysis View)
# User should be able to associate external files with events (excel spreadsheet, documents, etc.) (Operation View)
# Application will track status of consumables: (Operation View)
## Pucks
## Reagents: 20 or so
## Waste
## Power
# After planning, application should generate mission script, puck loads, and reagent volumes. (Operation View)
# Users should have a form to add/delete/edit protocol runs and phases. (Operation View)
# Users should have a form to add/delete/edit consumables. (Operation View)
# In application users should have sample volume listed with protocol run (Operation View)
# When users selects a protocol run/phase, the contextual data (CTD/ISUS) should somehow be shown. (Operation/Data Analysis View)
# Tide and phase information should be available during planning. (Operation View)
# Application should allow for details of flushes to be seen/accounted for. (Operation View)
# Users should be able to schedule Kills (end purges) or disable kills. (Operation View)
# Users should be able to define generic events and what script will actually be added to the master script (if needed). (Operation View)
# Users should be able to visualize the current state of the instrument. (Operation View)
# Users should be able to scroll back in time and visualize instrument state at the various points in time. (Operations View)
{column}
{column:width=40%}
{panel:title=Meeting Notes}
# [PDR Notes|Project Memos Minutes]
# [Meeting with Chris, June 11, 2007]
# [ESP GUI Demo and Questions|2007_09_05]
# [Follow up meeting on Resources and Consumables|2008_01_08]
# [Mock Mission Planning Meeting|2008_03_11]
{panel}
{panel:title=Supporting Docs}
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering member to try to determine what the GUI needs to do.  The following requirements were gathered as part of that process:

{section}
{column:width=60%}
h3. Requirements
||Number||Requirement||Associated View||
|1|User can define missions by specifying phases|Planning|
|2|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|Be able to add non-phase/protocol events (user defined) to the calendar anywhere|Operation|
|5|Be able to set mission start end times that are not associated with a phase/protocol|Planning|
|6|Be able to specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User shall be able to add comments to a phase that will be generated in the script|Planning|
|8|User shall be able to view images associated with phases|Operation|
|9|User shall be able to browse the .GAL file along with image and filter paper information|Operation|
|10|User should be able to browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Operation|
|11|User should be able to browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Operation|
|12|User should be able to associate external files with events (excel spreadsheet, documents, etc.)|Planning,Operation|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|Operation|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users should have a form to add/delete/edit protocol runs and phases|Planning|
|16|Users should have a form to add/delete/edit consumables|Planning|
|17|In application users should have sample volume listed with protocol run|Planning|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should somehow be shown|Operation|
|19|Tide and phase information should be available during planning|Planning,Operation|
|20|Application should allow for details of flushes to be seen/accounted for|Operation|
|21|Users should be able to schedule Kills (end purges) or disable kills|Planning|
|22|Users should be able to define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to visualize the current state of the instrument|Operation,State|
|24|Users should be able to scroll back in time and visualize instrument state at the various points in time|State|
{column}
{column:width=40%}
{panel:title=Meeting Notes}
# [PDR Notes|Project Memos Minutes]
# [Meeting with Chris, June 11, 2007]
# [ESP GUI Demo and Questions|2007_09_05]
# [Follow up meeting on Resources and Consumables|2008_01_08]
# [Mock Mission Planning Meeting|2008_03_11]
{panel}
{panel:title=Supporting Docs}
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application
{panel}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation
### Three stages:
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
{jiraissues:https://oceana.mbari.org/jira/sr/jira.issueviews:searchrequest-xml/temp/SearchRequest.xml?&pid=10050&status=1&status=3&status=4&component=10082&sorter/field=issuekey&sorter/order=DESC&sorter/field=priority&sorter/order=DESC&tempMax=1000|anonymous=true}
{panel}
h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]


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<property name="body"><![CDATA[The requirements for the ESP GUI and the process for how those were derived are documented here.  Meetings were held as well as several iterative development cycles as the process for gathering these requirements.

h3. Requirements
# [Requirements]

h3. Meeting Notes
# [PDR Notes|Project Memos Minutes]
# [Meeting with Chris, June 11, 2007]
# [ESP GUI Demo and Questions|2007_09_05]
# [Follow up meeting on Resources and Consumables|2008_01_08]
# [Mock Mission Planning Meeting|2008_03_11]

h3. Supporting Documents
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce. Divers: Kim R., Paul C.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

Divers: Paul C., Jeff Sevadjian

{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload. Divers: Eric R, Jeff Sevadjian
\\

h4. {color:#ff00cc}1st MAKAI flight w 5 cartridges{color}

*July 22, 2015*

Flew triangle pattern after launch.&nbsp; Makai found chlorophyll feature, and we fired two cartridges while flying through.&nbsp; First cartridge may have had sticky valve and stayed in by-pass (filtered 1L in \~20 minutes; too fast).&nbsp; Second cartridge seemed to have worked.

Some issues with ESP not communicating it was on, and then LRAUV not turning it on.&nbsp; Went to recover vehicle late July 23, but did not surface until mission timed-out, after we were already ashore.&nbsp; That was when we discovered the comms issues.&nbsp; Fixed one, tried to fire during a 'night operation' Thursday evening.&nbsp; Discovered Friday morning a second comms issues, which was fixed, and fired the 3 samples during day on Friday, July 24.&nbsp; Did keep-station all weekend, and recovered LRAUV early Monday morning (July 27).


Results:

1.&nbsp; Cartridge #1 bypassed 1L (toroid valve stuck; sea water ran through instrument in bypass mode; 7 minutes); flying through feature (chl=3.0 ug/l; 10.97m)


2. &nbsp; #2 filtered 815.8ml; flying through feature (11.03m; chl=3.3 ug/l; took 53 minutes)


3. &nbsp; #3 filtered 802.3ml;&nbsp; within feature (13.8m; chl=3.02 ug/l; took 51 minutes)


4. &nbsp; #4 filtered 759.6ml,&nbsp; above feature (7.1m; chl=1.11 ug/l; took 50 minutes)


5.&nbsp;&nbsp; #5 filtered 809.1ml,&nbsp; below feature (19.4m; chl=4.24 ug/l; took 51 minutes)]]></property>
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<property name="body"><![CDATA[The requirements for the ESP GUI and the process for how those were derived are documented here.  Meetings were held as well as several iterative development cycles as the process for gathering these requirements.

h3. Requirements
# [Requirements]
# User can define missions by specifying phases. (Operation View)
# User can specify and adjust phase start times. (Operation View)
# User can also specify a time to wait between events instead of a specific start time. (Operation View)
# Be able to add non-phase/protocol events (user defined) to the calendar anywhere. (Operation View)
# Be able to set mission start end times that are not associated with a phase/protocol. (Operation View)
# Be able to specify comments associated with missions that are printed at the top of the mission script. (Operation View)
# User shall be able to add comments to a phase that will be generated in the script. (Operation View)
# User shall be able to view images associated with phases. (Operation/Data Analysis View)
# User shall be able to browse the .GAL file along with image and filter paper information. (Operation/Data Analysis View)
# User should be able to browse image, click on intensity and application applies .GAL/Map with standard curves to give density. (Data Analysis)
# User should be able to browse the low-res images that come over the telemetry until full size image is offloaded after recovery. (Operation/Data Analysis View)
# User should be able to associate external files with events (excel spreadsheet, documents, etc.) (Operation View)
# Application will track status of consumables: (Operation View)
## Pucks
## Reagents: 20 or so
## Waste
## Power
# After planning, application should generate mission script, puck loads, and reagent volumes. (Operation View)
# Users should have a form to add/delete/edit protocol runs and phases. (Operation View)
# Users should have a form to add/delete/edit consumables. (Operation View)
# In application users should have sample volume listed with protocol run (Operation View)
# When users selects a protocol run/phase, the contextual data (CTD/ISUS) should somehow be shown. (Operation/Data Analysis View)
# Tide and phase information should be available during planning. (Operation View)
# Application should allow for details of flushes to be seen/accounted for. (Operation View)
# Users should be able to schedule Kills (end purges) or disable kills. (Operation View)
# Users should be able to define generic events and what script will actually be added to the master script (if needed). (Operation View)
# Users should be able to visualize the current state of the instrument. (Operation View)
# Users should be able to scroll back in time and visualize instrument state at the various points in time. (Operations View)

h3. Meeting Notes
# [PDR Notes|Project Memos Minutes]
# [Meeting with Chris, June 11, 2007]
# [ESP GUI Demo and Questions|2007_09_05]
# [Follow up meeting on Resources and Consumables|2008_01_08]
# [Mock Mission Planning Meeting|2008_03_11]

h3. Supporting Documents
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
]]></property>
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<property name="body"><![CDATA[{section}
{column:width=60%}
{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{column}
{section}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation
### Three stages:
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{column}
{section}
{panel:title=Bug Tracking}
{jiraissues:https://oceana.mbari.org/jira/sr/jira.issueviews:searchrequest-xml/temp/SearchRequest.xml?&pid=10050&component=10082&sorter/field=issuekey&sorter/order=DESC&sorter/field=priority&sorter/order=DESC&tempMax=1000|anonymous=true}
{panel}
h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]


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<property name="body"><![CDATA[{section}
{column:width=60%}
{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{column}
{section}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation
### Three stages:
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{column}
{section}
{panel:title=Bug Tracking}
{jiraissues:https://oceana.mbari.org/jira/sr/jira.issueviews:searchrequest-xml/temp/SearchRequest.xml?&pid=10050&status=1&status=3&status=4&component=10082&sorter/field=issuekey&sorter/order=DESC&sorter/field=priority&sorter/order=DESC&tempMax=1000|anonymous=true}
{panel}
h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]


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<property name="body"><![CDATA[{section}
{column:width=60%}
{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{column}
{section}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation
### Three stages:
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
{jiraissues:https://oceana.mbari.org/jira/sr/jira.issueviews:searchrequest-xml/temp/SearchRequest.xml?&pid=10050&status=1&status=3&status=4&component=10082&sorter/field=issuekey&sorter/order=DESC&sorter/field=priority&sorter/order=DESC&tempMax=1000|anonymous=true}
{panel}
h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]


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<property name="body"><![CDATA[h1. Meeting to discuss ESP Phases, Protocol Runs, and Consumables


h3. Attendees:

# Kevin Gomes
# Roman Marin
# Jim Birch
# Chris Preston
# Chris Scholin

h3. Agenda

The focus of this meeting is to identify all the appropriate phases, protocol runs and consumables and their amounts (recipies) that will be available for planning a mission on an ESP instrument.

h3. List from previous meeting


h5. Instruments:

# NEO
# GIGI
# Bruce
# Mack

h5. Lists of phases, protocols

All phases have flush intake, PHASE, then kill/end purge (can call out whether or not you want kill).&nbsp;
# HAB
## SH1
## lyfil
## SH2
## WCR
# DA
## DA1
## Dalyfil
## DA2
# BAC
## SH1
## lyfil
## SH2
## WCR
# invert
## SH1
## lyfil
## SH2
## WCR
# BACAR
## WCR
# QC
## WCR
# HABDA
## HAB phase
## DA phase

Other protocols:
# Flush
# Kill/end purge

These can both be skipped in certain situations.

h5. Details for phases:

# Max duration - all phases assume 1L sample, roughly 4 hours.&nbsp; HABDA would be about 6 hours.

h5. Details for protocols:

# Duration
# Delay to sample

h5. Consumable Types:

# Fix
# AqMeOH
# ab1
# ab2
# Lysis
# Diluent
# Sig1
# Sig2
# Sig3
# Con
# Sub 1
# Sub 2
# Wash
# CSR Flush (combine with CSV)
# CSV Flush
# PSR Flush
# Kill
# Waste1 (non-alcohol)
# Waste2 (alcohol)
# Power

h5. Bags/Containers/Storage:

# For NEO, how big are the capacities for the above consumables? (max volume is 2L)

h5. Protocol/Consumable Details (for each of the phase/protocol combination, what consumables do they use and how much?)

# Excel Spreadsheet?

h5. Mission Script Syntax (Work with Brent Roman)]]></property>
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<property name="body"><![CDATA[h5. Comments

# Have capability to add comments to phases that show up in script. Maybe go out in log too. Also add header comments. (global too).
# Modify protocol so it doesn't kill between phases (want capability to call out alternate purge).
# Always odd things (give it ruby and time to run and it puts it in script).
# Phases should be different colors
# BUG: If delete last phase, can't add one at end.
# Need to specify a way just to sequence things, not deterministic time. Or say, I just want to wait 15 minutes after it finishes.
# Have way to call out initial purge instead of upper/lowercase

h5. Questions

# How are volumes for duplicate phases handled?
{noformat}
# Sample Volumes for Assay Types
$habVol=1000
$larvVol=900
$larvVol=700
$daVol=30

startTube 2
# require '08feb'


startAt "14:44:34 03/12/2008"

initialPurge
hab
napUntil "10:05:13 03/13/2008"

larv
napUntil "05:50:00 03/14/2008"

initialPurge
larv
napUntil "17:45:00 03/14/2008"

da
shutdown
{noformat}
# Script gets generated but not in sync with timing of simulator/instrument, how to best synch:
{noformat}
CH.stop
I2C::MsgErr in sampler -- I2C::Servo::OffCmd Not yet modeled
I2C::MsgErr in storage -- I2C::Servo::OffCmd Not yet modeled
I2C::MsgErr in sampler -- I2C::Servo::ConfigureCmd Not yet modeled
I2C::MsgErr in storage -- I2C::Servo::ConfigureCmd Not yet modeled
CH.configure CHconfig
PH.stop
PH.configure PHconfig
Posix::Error in quick -- /dev/ctd not a character device
Starting with tube #2
delayUntil "06:15:00.00 PDT 13-Mar-08"
@06:15:00.00PDT13-Mar-08 <poll> CTD.startLogging
@06:15:00.00 <quick> Initial Intake Purge
@06:16:30.00 ==> hab 1000ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@09:46:30.00 Disinfect Intake
@09:48:30.00 Shutdown
delayUntil "13:50:00.00"
@12:15:00.00 <poll> CTD.update
@13:50:00.00 <quick> ==> bac 900ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@17:20:00.00 Disinfect Intake
@17:22:00.00 Shutdown
delayUntil "01:25:00.00 PDT 14-Mar-08"
@18:15:00.00 <poll> CTD.update
@00:15:00.00PDT14-Mar-08 CTD.update
@01:25:00.00 <quick> Initial Intake Purge
@01:26:30.00 ==> larv 900ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@04:56:30.00 Disinfect Intake
@04:58:30.00 Shutdown
delayUntil "11:20:00.00"
@06:15:00.00 <poll> CTD.update
@11:20:00.00 <quick> Initial Intake Purge
@11:21:30.00 ==> da 1000ml, :image=>[:hires, 15, :default, 4, :midres, :auto]
@12:15:00.00 <poll> CTD.update
@14:21:30.00 <quick> Disinfect Intake
@14:23:30.00 Shutdown
delayUntil "20:30:00.00"
@18:15:00.00 <poll> CTD.update
@20:30:00.00 <quick> Initial Intake Purge
@20:31:30.00 ==> hab 1000ml, :image=>[:hires, 160, :default, 40, :midres, :auto]
@00:01:30.00PDT15-Mar-08 ==> da 1000ml, :image=>[:hires, 15, :default, 4, :midres, :auto]
@00:15:00.00 <poll> CTD.update
@02:01:30.00 <quick> Disinfect Intake
@02:03:30.00 Shutdown
gui_test.rb Assays Completed. CTD logging continues ... 
delayUntil "00:13:07.00"
Schedule::Error in quick -- Delay::RunEvent for @00:13:07.00 PDT 15-Mar-08 is in the past
Waiting to Resume from Checkpoint "gui_test.rb Assays Completed. CTD logging continues ... "
@06:15:00.00 <poll> CTD.update
@12:15:00.00 CTD.update
@18:15:00.00 CTD.update
@00:15:00.00PDT16-Mar-08 CTD.update
{noformat}]]></property>
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<property name="body"><![CDATA[h3. Minutes from ESP GUI Demo and Question and Answer Session

The purpose of this meeting is to show the progress to date on the ESP Data Management/Planning GUI and to use this demonstration to foster information gathering that can be used to both direct development and answer development questions.
{section}
{column:width=60%}
h5. Data needed
# List of all possible consumable resources:
## Instruments:
### Darlene
### GIGI
### NEO
## Lists of phases, protocols
### HAB
#### SH1
#### lyfil
#### SH2
#### WCR
### DA
#### DA1
#### Dalyfil
#### DA2
### BAC
#### SH1
#### lyfil
#### SH2
#### WCR
### invert
#### SH1
#### lyfil
#### SH2
#### WCR
### BACAR
#### WCR
### QC
#### WCR
## Details for phases:
### Max duration
## Details for protocols:
### Duration
### Delay to sample
## Consumable Types:
### Fix
### AgMeOH
### ab1
### ab2
### Lysis
### Dilutent
### Sig1
### Sig2
### Sig3
### Con 1:5000
### Sub 1
### Sub 2
### Wash
### CSR Flush
### CSV Flush
### PSR Flush
### Kill
### Waste
### Power
## Bags/Containers/Storage:
### How big are the capacities for the above consumables?
## Protocol Makeup
### For each of the phase/protocol combination, what consumables to they use and how much (i.e. recipies)

{panel:title=New Requests From Meeting}
# Link the colors of the instruments to the deployments
# Have the deployments disappear on the overall calendar as well as the main calendar
# Clean up the view on the overview calendar so they don't look so busy (remove protocols and phases)
# Darlene is no longer with us, just GG (or GiGi) and Neo.  But there should be three new instruments coming on line.
# In the details pane, there was a desire to put the sample volume right next to the protocol name.
# When you select a protocol line in the details pane, a tab should be available to show the contextual data (CTD, ISUS) for the time span of when the sample volume was drawn
# There was a desire to have the CTD data displayed like the tide data is displayed and some way to turn on/off view of it
# Look into the possibility of using jruby to generate the mission script so the generation could be done outside of the planning application and changed there instead of inside the planning app.
## As a side note, you need to know the start tube in order to generate the mission script and the start tube will not be known till after the instrument is loaded.  Question, can't we tell the user how to best load the instrument based on the deployment configuration?
# There was a bit of discussion on the consumables view and how to use it in the planning phase.  I think the following was the resulting desire:
## When creating a new plan (deployment), the consumables should simply show how much of each consumable is being predicted (ml, watts, waste generation)
## Then at some point, the instrument will be 'loaded' and the view should be changed/enable that shows the amount of consumables are available (maybe also show how much is predicted to be consumed).  A full load will show all progress bars as 100% (display will show appropriate units like ml or watts) and then the bars will decrease as the log file is read and the actual amounts consumed are known.
## There was also a desire to know how many of the different phases could be configured with the current state of the instrument.  This speaks to the 'interrupted deployment scenario' where the instrument would be recovered and could be reconfigured (but no consumables added).  For example, if the instrument was recovered and it was half way through its consumption, the user could ask the application how many of the different phases could be run.  This would entail changing the pucks around, but the consumables would be left alone.  There was some talk about that just simply constituting a new 'deployment' since a new mission script would be created anyway.
{panel}
{column}
{column:width=40%}
{panel:title=Agenda}
# Introduction/Recap
# Demonstrate GUI to date
## How to start it.  Click here: [http://predator.shore.mbari.org/esp_gui/launch.jnlp]
## Should work on Java 1.5+
## Right now you will need to be connected to MBARI intranet (that will change to local laptop installation)
## Upper left is list of instruments and their associated deployment.  Default start is to have all displayed.
### Display selection tree functionality
## Year selection drives the overview calendar displayed below.
## The overview calendar always shows all deployments
## Click on overview calendar to select month of interest.
### This drives main calendar.
{panel}
{panel:title=Questions to Answer}
For GUI:
# Default is to have no deployments displayed.  Is that OK, or should have they all show up to begin with?
# Should I show all deployments on the overview calendar?
# Should consumables be decreasing meters and turn red on low?
# How much detail (zoom) do you want to see?
# Where do you want to edit phases/deployment (table/popup/etc.)?
For Mission Scripts:
# What is 'startTube' and how is it determined?
# What are the 'rules' around script construction? 
{panel}
{column}
{section}




h5. Comments

[~brian] We have the database modeled to support ESP from planning through analysis. My take though is that we should create discrete applications for the different phases of the ESP deployment lifecycle (Plan, manage, analyze). There are a lot of _like to have_ features so we should manage the user expectations and tell them what is possible to do in the short amount of time that we have.. We're currently focusing on the planning/script generation phase, which I think is appropriate. Everything else should be deferred until we get a solid planning app put together....just my 2 cents.]]></property>
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<property name="body"><![CDATA[h3. Minutes from ESP GUI Demo and Question and Answer Session

The purpose of this meeting is to show the progress to date on the ESP Data Management/Planning GUI and to use this demonstration to foster information gathering that can be used to both direct development and answer development questions.
{section}
{column:width=60%}
h5. Data needed
# List of all possible consumable resources:
## Instruments:
### Darlene
### GIGI
### NEO
## Lists of phases, protocols
### HAB
#### SH1
#### lyfil
#### SH2
#### WCR
### DA
#### DA1
#### Dalyfil
#### DA2
### BAC
#### SH1
#### lyfil
#### SH2
#### WCR
### invert
#### SH1
#### lyfil
#### SH2
#### WCR
### BACAR
#### WCR
### QC
#### WCR
## Details for phases:
### Max duration
## Details for protocols:
### Duration
### Delay to sample
## Consumable Types:
### Fix
### AgMeOH
### ab1
### ab2
### Lysis
### Dilutent
### Sig1
### Sig2
### Sig3
### Con 1:5000
### Sub 1
### Sub 2
### Wash
### CSR Flush
### CSV Flush
### PSR Flush
### Kill
### Waste
### Power
## Bags/Containers/Storage:
### How big are the capacities for the above consumables?
## Protocol Makeup
### For each of the phase/protocol combination, what consumables to they use and how much (i.e. recipies)
{panel:title=New Requests From Meeting}
# Link the colors of the instruments to the deployments
# Have the deployments disappear on the overall calendar as well as the main calendar
# Clean up the view on the overview calendar so they don't look so busy (remove protocols and phases)
# Darlene is no longer with us, just GG (or GiGi) and Neo.  But there should be three new instruments coming on line.
# In the details pane, there was a desire to put the sample volume right next to the protocol name.
# When you select a protocol line in the details pane, a tab should be available to show the contextual data (CTD, ISUS) for the time span of when the sample volume was drawn
# There was a desire to have the CTD data displayed like the tide data is displayed and some way to turn on/off view of it
# Look into the possibility of using jruby to generate the mission script so the generation could be done outside of the planning application and changed there instead of inside the planning app.
## As a side note, you need to know the start tube in order to generate the mission script and the start tube will not be known till after the instrument is loaded.  Question, can't we tell the user how to best load the instrument based on the deployment configuration?
# There was a bit of discussion on the consumables view and how to use it in the planning phase.  I think the following was the resulting desire:
## When creating a new plan (deployment), the consumables should simply show how much of each consumable is being predicted (ml, watts, waste generation)
## Then at some point, the instrument will be 'loaded' and the view should be changed/enable that shows the amount of consumables are available (maybe also show how much is predicted to be consumed).  A full load will show all progress bars as 100% (display will show appropriate units like ml or watts) and then the bars will decrease as the log file is read and the actual amounts consumed are known.
## There was also a desire to know how many of the different phases could be configured with the current state of the instrument.  This speaks to the 'interrupted deployment scenario' where the instrument would be recovered and could be reconfigured (but no consumables added).  For example, if the instrument was recovered and it was half way through its consumption, the user could ask the application how many of the different phases could be run.  This would entail changing the pucks around, but the consumables would be left alone.  There was some talk about that just simply constituting a new 'deployment' since a new mission script would be created anyway.
{panel}
{column}
{column:width=40%}
{panel:title=Agenda}
# Introduction/Recap
# Demonstrate GUI to date
## How to start it.  Click here: [http://predator.shore.mbari.org/esp_gui/launch.jnlp]
## Should work on Java 1.5+
## Right now you will need to be connected to MBARI intranet (that will change to local laptop installation)
## Upper left is list of instruments and their associated deployment.  Default start is to have all displayed.
### Display selection tree functionality
## Year selection drives the overview calendar displayed below.
## The overview calendar always shows all deployments
## Click on overview calendar to select month of interest.
### This drives main calendar.
{panel}
{panel:title=Questions to Answer}
For GUI:
# Default is to have no deployments displayed.  Is that OK, or should have they all show up to begin with?
# Should I show all deployments on the overview calendar?
# Should consumables be decreasing meters and turn red on low?
# How much detail (zoom) do you want to see?
# Where do you want to edit phases/deployment (table/popup/etc.)?
For Mission Scripts:
# What is 'startTube' and how is it determined?
# What are the 'rules' around script construction? 
{panel}
{column}
{section}




h5. Comments

[~brian] We have the database modeled to support ESP from planning through analysis. My take though is that we should create discrete applications for the different phases of the ESP deployment lifecycle (Plan, manage, analyze). There are a lot of _like to have_ features so we should manage the user expectations and tell them what is possible to do in the short amount of time that we have.. We're currently focusing on the planning/script generation phase, which I think is appropriate. Everything else should be deferred until we get a solid planning app put together....just my 2 cents.]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce. Divers: Kim R., Paul C.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

Divers: Paul C., Jeff Sevadjian

{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload. Divers: Eric R, Jeff Sevadjian
\\

h4. {color:#ff00cc}1st MAKAI flight w 5 cartridges{color}

*July 22, 2015*

Flew triangle pattern after launch.&nbsp; Makai found chlorophyll feature, and we fired two cartridges while flying through.&nbsp; First cartridge may have had sticky valve and stayed in by-pass (filtered 1L in \~20 minutes; too fast).&nbsp; Second cartridge seemed to have worked.

Next day fired three but algorithm did not have the flexibility to deal with layer crunched up on the surface. &nbsp;\\

Recovered July 23 late in day. ]]></property>
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<property name="body"><![CDATA[h3. Minutes from ESP GUI Demo and Question and Answer Session

The purpose of this meeting is to show the progress to date on the ESP Data Management/Planning GUI and to use this demonstration to foster information gathering that can be used to both direct development and answer development questions.
{section}
{column:width=60%}
h5. Data needed
# List of all possible consumable resources:
## Instruments:
### Darlene
### GIGI
### NEO
## Lists of phases, protocols
### HAB
#### SH1
#### lyfil
#### SH2
#### WCR
### DA
#### DA1
#### Dalyfil
#### DA2
### BAC
#### SH1
#### lyfil
#### SH2
#### WCR
### invert
#### SH1
#### lyfil
#### SH2
#### WCR
### BACAR
#### WCR
### QC
#### WCR
## Details for phases:
### Max duration
## Details for protocols:
### Duration
### Delay to sample
## Consumable Types:
### Fix
### AgMeOH
### ab1
### ab2
### Lysis
### Dilutent
### Sig1
### Sig2
### Sig3
### Con 1:5000
### Sub 1
### Sub 2
### Wash
### CSR Flush
### CSV Flush
### PSR Flush
### Kill
### Waste
### Power
## Bags/Containers/Storage:
### How big are the capacities for the above consumables?
## Protocol Makeup
### For each of the phase/protocol combination, what consumables to they use and how much (i.e. recipies)
{column}
{column:width=40%}
{panel:title=Agenda}
# Introduction/Recap
# Demonstrate GUI to date
## How to start it.  Click here: [http://predator.shore.mbari.org/esp_gui/launch.jnlp]
## Should work on Java 1.5+
## Right now you will need to be connected to MBARI intranet (that will change to local laptop installation)
## Upper left is list of instruments and their associated deployment.  Default start is to have all displayed.
### Display selection tree functionality
## Year selection drives the overview calendar displayed below.
## The overview calendar always shows all deployments
## Click on overview calendar to select month of interest.
### This drives main calendar.
{panel}
{panel:title=Questions to Answer}
For GUI:
# Default is to have no deployments displayed.  Is that OK, or should have they all show up to begin with?
# Should I show all deployments on the overview calendar?
# Should consumables be decreasing meters and turn red on low?
# How much detail (zoom) do you want to see?
# Where do you want to edit phases/deployment (table/popup/etc.)?
For Mission Scripts:
# What is 'startTube' and how is it determined?
# What are the 'rules' around script construction? 
{panel}
{column}
{section}
{panel:title=New Requests From Meeting}
# Link the colors of the instruments to the deployments
# Have the deployments disappear on the overall calendar as well as the main calendar
# Clean up the view on the overview calendar so they don't look so busy (remove protocols and phases)
# Darlene is no longer with us, just GG (or GiGi) and Neo.  But there should be three new instruments coming on line.
# In the details pane, there was a desire to put the sample volume right next to the protocol name.
# When you select a protocol line in the details pane, a tab should be available to show the contextual data (CTD, ISUS) for the time span of when the sample volume was drawn
# There was a desire to have the CTD data displayed like the tide data is displayed and some way to turn on/off view of it
# Look into the possibility of using jruby to generate the mission script so the generation could be done outside of the planning application and changed there instead of inside the planning app.
## As a side note, you need to know the start tube in order to generate the mission script and the start tube will not be known till after the instrument is loaded.  Question, can't we tell the user how to best load the instrument based on the deployment configuration?
# There was a bit of discussion on the consumables view and how to use it in the planning phase.  I think the following was the resulting desire:
## When creating a new plan (deployment), the consumables should simply show how much of each consumable is being predicted (ml, watts, waste generation)
## Then at some point, the instrument will be 'loaded' and the view should be changed/enable that shows the amount of consumables are available (maybe also show how much is predicted to be consumed).  A full load will show all progress bars as 100% (display will show appropriate units like ml or watts) and then the bars will decrease as the log file is read and the actual amounts consumed are known.
## There was also a desire to know how many of the different phases could be configured with the current state of the instrument.  This speaks to the 'interrupted deployment scenario' where the instrument would be recovered and could be reconfigured (but no consumables added).  For example, if the instrument was recovered and it was half way through its consumption, the user could ask the application how many of the different phases could be run.  This would entail changing the pucks around, but the consumables would be left alone.  There was some talk about that just simply constituting a new 'deployment' since a new mission script would be created anyway.
{panel}




h5. Comments

[~brian] We have the database modeled to support ESP from planning through analysis. My take though is that we should create discrete applications for the different phases of the ESP deployment lifecycle (Plan, manage, analyze). There are a lot of _like to have_ features so we should manage the user expectations and tell them what is possible to do in the short amount of time that we have.. We're currently focusing on the planning/script generation phase, which I think is appropriate. Everything else should be deferred until we get a solid planning app put together....just my 2 cents.]]></property>
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<property name="body"><![CDATA[# Attendees
## Chris Scholin
## Rich Schramm
## Brian Schlining
## Karen Salamy
## Kevin Gomes

# Notes
## Phases: HAB, BAC, LARV
## Phases run protocols
## Phase is a series of operations (could be one protocol, but more likely more).  Can be one puck, but more likely more.
## Phase is a standard set of operations
## Each protocol needs a puck (with filter)
## Filter may or may not have probes, whole cell has no probes, just brings home sample
## All pucks have serial numbers.
## pucks outer diameter is the same.
## there are different pucks for different
## SH = standard hybridization, detect molecules of interest. Heat it up and liquify.  Filter and then apply to SH2.  SH1 pucks can be used lysate.
## Why do we want to keep track of serial numbers on pucks
## Once puck is closed, not sure what is in there.
## Serial numbers help keep track of what they intend to use it for after build.
## Some have physical specimen and they need to figure out which puck has the specimen
## After filteration, put on another filter, then more chemistry, then image.
## Final PUCK is WCR (whole cell archival) is then sample is then preserved and brought home for shore side analysis
## Associated with probes is spot map (array map) ".Gal File" (what probe in what X,Y location).  Often listed as "Spot 23" then lookup with tell you X,Y
## Image is analyzed and you get intensities.
## Device can do "auto exposure" to figure out where it needs to be to get image in linear range of CCD chip.
## Also ask for constant exposure (do more than one constant exposure).
## Use standard curves and control spots on map.
## Standard curve is number of bugs/intensity
## Run exposure that you have standard curve for and then get intensity which then you lookup on the spot map.
## Low res images come across the wire (high res is 1MB).
## Phases can change the protocols (should we force users to use unique names- Chris thinks this would be good)
## Array map evolves.
## Protocols use same reagants, same amount 
## Phase-protocol combination (Phase tells you what the amounts are in the different protocols)
## Volumes filtered varies (tell it "Collect a liter", instrument decides how much until to filter until clogged)
## Print info comes from "gal file".  Old print is excel file.
## Some filters are thrown away, some are archived.
## Comments also need to be captured.
## Events are "when we sample"
## User specifies start of phase
### Then delay (7 minutes let's say), then sample is taken (that is the actual "start").  The rest of the protocols depend on the environmental characteristics.
## There will be maximum time for each phase (can be shorter, never longer).
## Instrument capacities:
### Pucks: 
### Reagants: 20
### Waste: fixed in current machine
## Configuration file tells what reagents are at what valve.
## There is a waste 1 and waste 2 (NOTE this is dependent on the reagent. specify which waste reagent goes to)
## Power budget.
## Instrument run
### Take series of protocol, to build phases
### write high level script
### derive max volumes.
## Number of pucks is usual limitation
## sometimes waste can be limiter.

# Questions
## does the delay (7 minutes) only happen at the beginning of each phase or each protocol?
## Is max duration at the phase level or protocol level?
## ]]></property>
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<property name="body"><![CDATA[h3. ESP GUI Demo and Question and Answer Session

The purpose of this meeting is to show the progress to date on the ESP Data Management/Planning GUI and to use this demonstration to foster information gathering that can be used to both direct development and answer development questions.

h5. Agenda

# Introduction/Recap
# Demonstrate GUI to date
## How to start it.  Click here: [http://predator.shore.mbari.org/esp_gui/launch.jnlp]
## Should work on Java 1.5+
## Right now you will need to be connected to MBARI intranet (that will change to local laptop installation)
## Upper left is list of instruments and their associated deployment.  Default start is to have all displayed.
### Display selection tree functionality
## Year selection drives the overview calendar displayed below.
## The overview calendar always shows all deployments
## Click on overview calendar to select month of interest.
### This drives main calendar.
 

h5. Questions:
# GUI:
## Default is to have no deployments displayed.  Is that OK, or should have they all show up to begin with?
## Should I show all deployments on the overview calendar?
## Should consumables be decreasing meters and turn red on low?
## How much detail (zoom) do you want to see?
## Where do you want to edit phases/deployment (table/popup/etc.)?
# Mission Scripts:
## What is 'startTube' and how is it determined?
## What are the 'rules' around script construction? 

h5. Data needed
# List of all possible consumable resources:
## Instruments:
### Darlene
### GIGI
### NEO
## Lists of phases, protocols
### HAB
#### SH1
#### lyfil
#### SH2
#### WCR
### DA
#### DA1
#### Dalyfil
#### DA2
### BAC
#### SH1
#### lyfil
#### SH2
#### WCR
### invert
#### SH1
#### lyfil
#### SH2
#### WCR
### BACAR
#### WCR
### QC
#### WCR
## Details for phases:
### Max duration
## Details for protocols:
### Duration
### Delay to sample
## Consumable Types:
### Fix
### AgMeOH
### ab1
### ab2
### Lysis
### Dilutent
### Sig1
### Sig2
### Sig3
### Con 1:5000
### Sub 1
### Sub 2
### Wash
### CSR Flush
### CSV Flush
### PSR Flush
### Kill
### Waste
### Power
## Bags/Containers/Storage:
### How big are the capacities for the above consumables?
## Protocol Makeup
### For each of the phase/protocol combination, what consumables to they use and how much (i.e. recipies)

h5. Requests
# Link the colors of the instruments to the deployments
# Have the deployments disappear on the overall calendar as well as the main calendar
# Clean up the view on the overview calendar so they don't look so busy (remove protocols and phases)
# Darlene is no longer with us, just GG (or GiGi) and Neo.  But there should be three new instruments coming on line.
# In the details pane, there was a desire to put the sample volume right next to the protocol name.
# When you select a protocol line in the details pane, a tab should be available to show the contextual data (CTD, ISUS) for the time span of when the sample volume was drawn
# There was a desire to have the CTD data displayed like the tide data is displayed and some way to turn on/off view of it
# Look into the possibility of using jruby to generate the mission script so the generation could be done outside of the planning application and changed there instead of inside the planning app.
## As a side note, you need to know the start tube in order to generate the mission script and the start tube will not be known till after the instrument is loaded.  Question, can't we tell the user how to best load the instrument based on the deployment configuration?
# There was a bit of discussion on the consumables view and how to use it in the planning phase.  I think the following was the resulting desire:
## When creating a new plan (deployment), the consumables should simply show how much of each consumable is being predicted (ml, watts, waste generation)
## Then at some point, the instrument will be 'loaded' and the view should be changed/enable that shows the amount of consumables are available (maybe also show how much is predicted to be consumed).  A full load will show all progress bars as 100% (display will show appropriate units like ml or watts) and then the bars will decrease as the log file is read and the actual amounts consumed are known.
## There was also a desire to know how many of the different phases could be configured with the current state of the instrument.  This speaks to the 'interrupted deployment scenario' where the instrument would be recovered and could be reconfigured (but no consumables added).  For example, if the instrument was recovered and it was half way through its consumption, the user could ask the application how many of the different phases could be run.  This would entail changing the pucks around, but the consumables would be left alone.  There was some talk about that just simply constituting a new 'deployment' since a new mission script would be created anyway.


h5. Comments

[~brian] We have the database modeled to support ESP from planning through analysis. My take though is that we should create discrete applications for the different phases of the ESP deployment lifecycle (Plan, manage, analyze). There are a lot of _like to have_ features so we should manage the user expectations and tell them what is possible to do in the short amount of time that we have.. We're currently focusing on the planning/script generation phase, which I think is appropriate. Everything else should be deferred until we get a solid planning app put together....just my 2 cents.]]></property>
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering member to try to determine what the GUI needs to do.  The following requirements were gathered as part of that process:

h3. Requirements
{section}
{column:width=60%}
||Number||Requirement||Associated View||
|1|User can define missions by specifying phases|Planning|
|2|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|Be able to add non-phase/protocol events (user defined) to the calendar anywhere|Operation|
|5|Be able to set mission start end times that are not associated with a phase/protocol|Planning|
|6|Be able to specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User shall be able to add comments to a phase that will be generated in the script|Planning|
|8|User shall be able to view images associated with phases|Operation|
|9|User shall be able to browse the .GAL file along with image and filter paper information|Operation|
|10|User should be able to browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Operation|
|11|User should be able to browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Operation|
|12|User should be able to associate external files with events (excel spreadsheet, documents, etc.)|Planning,Operation|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|Operation|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users should have a form to add/delete/edit protocol runs and phases|Planning|
|16|Users should have a form to add/delete/edit consumables|Planning|
|17|In application users should have sample volume listed with protocol run|Planning|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should somehow be shown|Operation|
|19|Tide and phase information should be available during planning|Planning,Operation|
|20|Application should allow for details of flushes to be seen/accounted for|Operation|
|21|Users should be able to schedule Kills (end purges) or disable kills|Planning|
|22|Users should be able to define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to visualize the current state of the instrument|Operation,State|
|24|Users should be able to scroll back in time and visualize instrument state at the various points in time|State|
{column}
{column:width=40%}
{panel:title=Meeting Notes}
# [PDR Notes|Project Memos Minutes]
# [Meeting with Chris, June 11, 2007]
# [ESP GUI Demo and Questions|2007_09_05]
# [Follow up meeting on Resources and Consumables|2008_01_08]
# [Mock Mission Planning Meeting|2008_03_11]
{panel}
{panel:title=Supporting Docs}
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering member to try to determine what the GUI needs to do.  The following requirements were gathered as part of that process:

h3. Requirements
{section}
{column:width=60%}
||Number||Requirement||Associated View||
|1|User can define missions by specifying phases|Planning|
|2|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|Be able to add non-phase/protocol events (user defined) to the calendar anywhere|Operation|
|5|Be able to set mission start end times that are not associated with a phase/protocol|Planning|
|6|Be able to specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User shall be able to add comments to a phase that will be generated in the script|Planning|
|8|User shall be able to view images associated with phases|Operation|
|9|User shall be able to browse the .GAL file along with image and filter paper information|Operation|
|10|User should be able to browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Operation|
|11|User should be able to browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Operation|
|12|User should be able to associate external files with events (excel spreadsheet, documents, etc.)|Planning,Operation|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|Operation|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users should have a form to add/delete/edit protocol runs and phases|Planning|
|16|Users should have a form to add/delete/edit consumables|Planning|
|17|In application users should have sample volume listed with protocol run|Planning|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should somehow be shown|Operation|
|19|Tide and phase information should be available during planning|Planning,Operation|
|20|Application should allow for details of flushes to be seen/accounted for|Operation|
|21|Users should be able to schedule Kills (end purges) or disable kills|Planning|
|22|Users should be able to define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to visualize the current state of the instrument|Operation,State|
|24|Users should be able to scroll back in time and visualize instrument state at the various points in time|State|
{column}
{column:width=40%}
{panel:title=Meeting Notes}
# [June 06, 2007 PDR|Project Memos Minutes]
# [June 11, 2007 Meet with Chris|Meeting with Chris, June 11, 2007]
# [Sept 05, 2007 ESP GUI Demo and Questions|2007_09_05]
# [Jan  08, 2008 Resources and Consumables|2008_01_08]
# [Mar 11, 2008 Mock Mission Planning Meeting|2008_03_11]
{panel}
{panel:title=Supporting Docs}
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h3. Project Information
# The project proposals can be found here:
## [2008|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
## [2009|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]


h3. The Application
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application

h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]

h3. Project Documentation:
# [Requirements (and Gathering)|Requirements (and Gathering) Documentation]
# [Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]

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<property name="body"><![CDATA[Meeting notes are no longer being maintained on Confluence. (sep 2012)
\\
# [Jan 31]
# [Feb  2]
# [Feb 14]]]></property>
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<property name="body"><![CDATA[Meeting notes are no longer being maintained on Confluence.
\\
# [Jan 31]
# [Feb  2]
# [Feb 14]]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application

h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]

h3. Project Documentation:
# [Requirements (and Gathering)|Requirements (and Gathering) Documentation]
# [Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]

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<property name="body"><![CDATA[# [Jan 31]
# [Feb  2]
# [Feb 14]]]></property>
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<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.

June 26 - continues to run, but lost internet access due to an unknown networking error.

h3. {color:#ff00ff}So. California Deployment of ESP-Gordon / NEO{color}

Aug 30 \-\- Haul instrument and gear in trailer and MBARI van to deploy on OCSD R/V Nerissa.  Calm seas, hot weather, instrument in \~10:30am.  Gordon w/PCR, CTD, ISUS, cell-phone modem (T-Mobile).  Sewage diversion to begin Sep 11, 2012. Machine located at 33.59703 \-117.94623


Kevan collecting data here: [http://www.stanford.edu/~kevany/ESP/].

Sep 14-noticed CTD battery draining faster than expected because of optode.&nbsp; Also, ATV encoder in MFB&nbsp; kept returning 511, which is 2**9-1&nbsp; meaning all bits are stuck high--typical way they fail.&nbsp; Stopped PCR, continued SHA, but with dead CTD no contextual data to adaptive sample off of.&nbsp; Decision to flip for NEO on Sep 26.

h3. {color:#ff00ff}Fall CANON--Drifter with ESP-Moe / Moe{color}

WF leaves MBARI Sept 10.&nbsp; Moe with PCR, ISUS, CTD, PAR, and buoy has downward ADCP.&nbsp; Roman and Julie R. on ship.

Moe went into water Sep 11. First phase slated for 6pm.

Pulled Sep 17 (10:30am).&nbsp; E/M cable started flaking out either due to connector or bad ethernet extender.&nbsp; Decision to end mission unrelated to this. ]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-1.2.1.jar] to your computer.
# Double-click the jar to run the app.

You can also get the automated image analysis application [here|http://www.mbari.org/staff/brian/software/esp-automated-imaging-0.3.jar]

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|Investigations into Automated Image Analysis].

I'm working on a new method. Documentation is [here|ESP Automated Image Analysis 2]

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter 
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size. 
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[h4. (as of May, 2014)


h3. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m (bare)*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

*21.5m*

Now (Apr 2014) with bad connector...
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos [here|^Image 3.jpg|corrosion] and [here|^Image 2.jpg|salt crystals].

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)

*15.2m*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h3. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]]]></property>
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<property name="body"><![CDATA[{section}
{column:width=60%}
{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{column}
{section}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation
### Three stages:
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{column}
{section}
{panel:title=Bug Tracking}
{jiraissues:url=https://oceana.mbari.org/jira/sr/jira.issueviews:searchrequest-xml/temp/SearchRequest.xml?&pid=10050&component=10082&sorter/field=issuekey&sorter/order=DESC&tempMax=1000|anonymous=true}
{panel}
h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]


]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce. Divers: Kim R., Paul C.


*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

Divers: Paul C., Jeff Sevadjian


{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload. Divers: Eric R, Jeff Sevadjian
\\

h4. {color:#ff00cc}Next{color}

*Set xx*]]></property>
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<property name="body"><![CDATA[{section}
{column:width=60%}
{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{column}
{section}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation
### Three stages:
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{column}
{section}
{panel:title=Bug Tracking}
{jiraissues:url=https://oceana.mbari.org/jira/sr/jira.issueviews:searchrequest-xml/temp/SearchRequest.xml?&pid=10050&component=10082&sorter/field=issuekey&sorter/order=DESC&tempMax=1000}
{panel}
h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]


]]></property>
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<property name="body"><![CDATA[{section}
{column:width=60%}
{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{column}
{section}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation
### Three stages:
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{panel:title=Bug Tracking}
{jiraissues:url=https://oceana.mbari.org/jira/sr/jira.issueviews:searchrequest-xml/temp/SearchRequest.xml?&pid=10050&component=10082&sorter/field=issuekey&sorter/order=DESC&tempMax=1000}
{panel}
{column}
{section}
h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]


]]></property>
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<property name="body"><![CDATA[{section}
{column:width=60%}
{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{column}
{section}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation
### Three stages:
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{column}
{section}
h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]


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{column}
{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application
{panel}
{column}
{column}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{column}
{section}
{section}
{column|width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation
### Three stages:
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column|width=40%}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{column}
{section}
h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]


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<property name="body"><![CDATA[{section}
{column}
{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application
{panel}
{column}
{column}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{column}
{section}
{section}
{column}
{panel:title=Goals Related to GUI}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation
### Three stages:
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column}
{panel:title|Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{column}
{section}
h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]


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<property name="body"><![CDATA[{section}
{column}
{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application
{panel}
{column}
{column}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{column}
{section}
{panel:title=Goals Related to GUI}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation
### Three stages:
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}


h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]

h3. Project Documentation:
# [Requirements (and Gathering)|Requirements (and Gathering) Documentation]
# [Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]

]]></property>
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{column}
{panel:title=Current Version of the Application}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application
{panel}
{column}
{column}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{column}
{section}
{panel:title=Goals Related to GUI}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation
### Three stages:
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}


h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]

h3. Project Documentation:
# [Requirements (and Gathering)|Requirements (and Gathering) Documentation]
# [Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]

]]></property>
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<property name="body"><![CDATA[{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}

{panel:title=Goals Related to GUI}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation
### Three stages:
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}

h3. The Application
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application

h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]

h3. Project Documentation:
# [Requirements (and Gathering)|Requirements (and Gathering) Documentation]
# [Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]

]]></property>
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<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.

June 26 - continues to run, but lost internet access due to an unknown networking error.

h3. {color:#ff00ff}So. California Deployment of ESP-Gordon / NEO{color}

Aug 30 \-\- Haul instrument and gear in trailer and MBARI van to deploy on OCSD R/V Nerissa.  Calm seas, hot weather, instrument in \~10:30am.  Gordon w/PCR, CTD, ISUS, cell-phone modem (T-Mobile).  Sewage diversion to begin Sep 11, 2012. Machine located at 33.59703 \-117.94623

Kevan collecting data here: [http://www.stanford.edu/~kevany/ESP/].

Sep 14-noticed CTD battery draining faster than expected because of optode.&nbsp; Also, ATV encoder in MFB&nbsp; kept returning 511, which is 2**9-1&nbsp; meaning all bits are stuck high--typical way they fail.&nbsp; Stopped PCR, continued SHA, but with dead CTD no contextual data to adaptive sample off of.&nbsp; Decision to flip for NEO on Sep 26.

Sep 26--recovered ESP-Gordon and swapped both batteries and ESP-Neo.&nbsp; Also changed CTD so now no optode (O2) measurments.&nbsp; One power cable fizzed away.&nbsp; Connector on pickle jar loose.&nbsp; But NEO now running well. Skipper gave deployment coordinates of 33 35.829 &nbsp; \-117 56.759.&nbsp; Xeos says&nbsp; 33.59702 \-117.94604.&nbsp; Water depth 18m.&nbsp; top of can depth


h3. {color:#ff00ff}Fall CANON--Drifter with ESP-Moe / Moe{color}

WF leaves MBARI Sept 10.&nbsp; Moe with PCR, ISUS, CTD, PAR, and buoy has downward ADCP.&nbsp; Roman and Julie R. on ship.

Moe went into water Sep 11. First phase slated for 6pm.

Pulled Sep 17 (10:30am).&nbsp; E/M cable started flaking out either due to connector or bad ethernet extender.&nbsp; Decision to end mission unrelated to this. ]]></property>
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<property name="body"><![CDATA[h3. Project Information
# The project proposals can be found here:
## [2007|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
## [2008|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
## [2009|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]

h3. Goals related to GUI
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation
### Three stages:
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)

h3. The Application
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application

h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]

h3. Project Documentation:
# [Requirements (and Gathering)|Requirements (and Gathering) Documentation]
# [Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]

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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-1.2.2.jar] to your computer.
# Double-click the jar to run the app.

You can also get the automated image analysis application [here|http://www.mbari.org/staff/brian/software/esp-automated-imaging-0.3.jar]

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|Investigations into Automated Image Analysis].

I'm working on a new method. Documentation is [here|ESP Automated Image Analysis 2]

h1. How to use it


h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls

!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.
{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size.
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result

!filter_3-20090430221134.png!

h3. Data Result

{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-1.2.3.jar] to your computer.
# Double-click the jar to run the app.

You can also get the automated image analysis application [here|http://www.mbari.org/staff/brian/software/esp-automated-imaging-0.3.jar]

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|Investigations into Automated Image Analysis].

I'm working on a new method. Documentation is [here|ESP Automated Image Analysis 2]

h1. How to use it


h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls

!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.
{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size.
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result

!filter_3-20090430221134.png!

h3. Data Result

{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.

Now you can run through the [ESP GUI Users Guide]
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


]]></property>
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<id name="id">26673536</id>
<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began?? and ended ~ week later when pump tore from piling.

*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).
Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays
Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

MELO used was #300034012090780

location reported by MELO was-\- &nbsp; 33.4865 \-118.51285

*March 20*\--lost comms

*March 21*\--re-established comms and think problem in E/M cable.

*March 22*\--lost comms

*April 3*\--small boat to buoy to test E/M cable

*April 8*\--'rescue' mission. Swapped E/M cables and repositioned in slightly deeper water, at 33.48504 \-118.50988

water depth 175m.&nbsp; top of can 10.9m

*RECOVERY--see below*

h4. {color:#ff00cc}ECOHAB--S. California{color}

*April 1*\--Instruments deployed

&nbsp;MOE--inshore at 33.60779 \-118.01877 with ISUS

Melo was 300234060014550

avg can depth \~9m
\\

&nbsp;Bruce--offshore at 33.58609 \-118.03686

Melo was 300234060016190

avg can depth \~19.5m

*~ April 9* lost communication with Bruce.&nbsp;

*April 15*\--Rescue mission w/Nerissa found 'hung' modem.&nbsp; Power cycled and checked cables on deck.&nbsp; Re-deployed in nearby spot.&nbsp; Divers (Kim R. & George M) measured 17.7m to top of can, 25.3 m to master link.

*RECOVERY*\--Plan was to pull ECOHAB April 30 with LBA0P divers off Nerissa, Catalina with Wrigley divers off Yellowfin May 1.&nbsp;&nbsp; April 30 had horrible Santa Ana winds; motored offshore to Bruce, and too rough.&nbsp; Cancelled entire day.&nbsp; Would try next day as winds supposed to die.&nbsp; Met at 5am and decided to cancel again, as winds were still blowing.&nbsp; Drove to Long Beach, and no wind up there. Salvaged that day by rounding up crew and wrigley divers after initially cancelling and heading over about noon.&nbsp; During that time, Dennis (skipper of Yellowfin) agreed to go the next day (Friday) to retrieve the two ECOHAB instruments.&nbsp; Eric Reinecker came down from MBARI, joining Jim Citanovich from SCMI and we retrieved Mack and Bruce.&nbsp; Back at SCMI around 1pm.&nbsp; Flatbed loaded by 4:30.&nbsp; Returned to MBARI next day (Saturday).]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.

Now you can run through the [ESP GUI Users Guide]
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


]]></property>
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</property>
</object>
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<id name="id">4489275</id>
<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">26673561</id>
<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began?? and ended ~ week later when pump tore from piling.

*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).
Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays
Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

MELO used was #300034012090780

location reported by MELO was-\- &nbsp; 33.4865 \-118.51285

*March 20*\--lost comms

*March 21*\--re-established comms and think problem in E/M cable.

*March 22*\--lost comms

*April 3*\--small boat to buoy to test E/M cable

*April 8*\--'rescue' mission. Swapped E/M cables and repositioned in slightly deeper water, at 33.48504 \-118.50988

water depth 175m.&nbsp; top of can 10.9m

*RECOVERY--see below*

h4. {color:#ff00cc}ECOHAB--S. California{color}

*April 1*\--Instruments deployed

&nbsp;MOE--inshore at 33.60779 \-118.01877 with ISUS

Melo was 300234060014550

avg can depth \~9m
\\

&nbsp;Bruce--offshore at 33.58609 \-118.03686

Melo was 300234060016190

avg can depth \~19.5m

*~ April 9* lost communication with Bruce.&nbsp;

*April 15*\--Rescue mission w/Nerissa found 'hung' modem.&nbsp; Power cycled and checked cables on deck.&nbsp; Re-deployed in nearby spot.&nbsp; Divers (Kim R. & George M) measured 17.7m to top of can, 25.3 m to master link.

*RECOVERY*\--Plan was to pull ECOHAB April 30 with LBA0P divers off Nerissa, Catalina with Wrigley divers off Yellowfin May 1.&nbsp;&nbsp; April 30 had horrible Santa Ana winds; motored offshore to Bruce, and too rough.&nbsp; Cancelled entire day.&nbsp; Would try next day as winds supposed to die.&nbsp; Met at 5am and decided to cancel again, as winds were still blowing.&nbsp; Drove to Long Beach, and no wind up there. Salvaged that day by rounding up crew and wrigley divers after initially cancelling and heading over about noon.&nbsp; During that time, Dennis (skipper of Yellowfin) agreed to go the next day (Friday) to retrieve the two ECOHAB instruments.&nbsp; Eric Reinecker came down from MBARI, joining Jim Citanovich from SCMI and we retrieved Mack and Bruce.&nbsp; Back at SCMI around 1pm.&nbsp; Flatbed loaded by 4:30.&nbsp; Returned to MBARI next day (Saturday).

h4. {color:#ff00cc}Sulfur Cycling (Moran)--Monterey Bay{color}

*Sep 15*\--Instrument deployed

&nbsp;ESP-Gordon--at 36.83113 \-121.91114&nbsp; (M0) with ISUS and CTD.&nbsp; Forgot to start Melo (did it next day).&nbsp; Running archive-only mission, ended up deeper than we had hoped (~12m instead of 7-10m).
\\]]></property>
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<id name="id">26673559</id>
<property name="body"><![CDATA[h4. (as of July, 2014)


h1. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m (bare)*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

*21.5m*

Now (Apr 2014) with bad connector...
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos [here|^Image 3.jpg|corrosion] and [here|^Image 2.jpg|salt crystals].

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)

*15.2m*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]

(shockles 1-4 used in SoCal ECOHAB-2013 and Monterey Bay ECOHAB-2013, but unclear which used when )


h4. ESP-001

* 44 days during Catalina (April 2014) deployment

h4. ESP-002
\\

h4. ESP-003

* &nbsp;32 days S. Cal ECOHAB w/Mack (Apr 2014)

h4. ESP-004

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).

h4. ESP-005


h1. Anchor lines
\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4.


h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\ \\]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.

Now you can run through the [ESP GUI Users Guide]
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# Use Cases
## [ESP Configuration In Lab]
## [Mission Planning for ESP]
## [ESP Deployment]
## [ESP Operations]
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process.

h3. Requirements
|| Number || Requirement || Goal ||
| | User can define missions by specifying phases | Planning |
| | User can specify and adjust phase start times | Planning |
| | User can also specify a time to wait between events instead of a specific start time | Planning |
| | User can set mission start and end times that are not associated with a phase/protocol | Planning |
| | User can specify comments associated with missions that are printed at the top of the mission script | Planning |
| | After planning, application should generate mission script, puck loads, and reagent volumes | Planning |
| | User can add comments to a phase that will be generated in the script | Planning |
| | Users can add/delete/edit protocol runs and phases | Planning |
| | Users can specify thresholding events in plans ([example|Mission Planning Script with Thresholding]) | Planning |
| | Users can copy existing phase and protocol to crate duplicate | Planning |
| | Users can add/delete/edit consumables | Planning |
| | Users can schedule Kills (end purges) or disable kills | Planning |
| | Users can define generic events and what script will actually be added to the master script (if needed) | Planning |
| | Mission plan generation will include a puck loading list | Planning |
| | User can associate external files with events (excel spreadsheet, documents, etc.) | Planning, Data Management |
| | Tide and phase information will be available | Planning, Data Management |
| | Application will list sample volumes with protocol run | Planning, Data Management |
| | User can add non-phase/protocol events (user defined) to the calendar anywhere | Data Management |
| | User can view images associated with phases | Data Management |
| | User can browse the .GAL file along with image and filter paper information | Data Management |
| | User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density | Data Management |
| | User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery | Data Management |
| | When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown | Data Management |
| | Application should allow for details of flushes to be seen/accounted for | Data Management |
| | The application should archive (and make available) the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts | Data Management |
| | Users should be able to download instrument logs and images and the GUI will parse out the following events:
* Track deployments of contextual sensors (sub-deployments of ESP)
* Collection of contextual sensor data (with capability to view/work with data) 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time | Data Management, State Visualization |
| | Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power | State Visualization |
| | Users can visualize the current state of the instrument | State Visualization |
| | Users can scroll back in time and visualize instrument state at the various points in time | State Visualization |

h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Glossary]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
# [01/11/2012 *GUI Update and Planning Meeting*|2011_01_12]
{panel}
{column}
{section}
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process.

h3. Requirements
|| Number || Requirement || Goal ||
| | User can define missions by specifying phases | Planning |
| | User can specify and adjust phase start times | Planning |
| | User can also specify a time to wait between events instead of a specific start time | Planning |
| | User can set mission start and end times that are not associated with a phase/protocol | Planning |
| | User can specify comments associated with missions that are printed at the top of the mission script | Planning |
| | After planning, application should generate mission script, puck loads, and reagent volumes | Planning |
| | User can add comments to a phase that will be generated in the script | Planning |
| | Users can add/delete/edit protocol runs and phases | Planning |
| | Users can copy existing phase and protocol to crate duplicate | Planning |
| | Users can add/delete/edit consumables | Planning |
| | Users can schedule Kills (end purges) or disable kills | Planning |
| | Users can define generic events and what script will actually be added to the master script (if needed) | Planning |
| | Mission plan generation will include a puck loading list | Planning |
| | User can associate external files with events (excel spreadsheet, documents, etc.) | Planning, Data Management |
| | Tide and phase information will be available | Planning, Data Management |
| | Application will list sample volumes with protocol run | Planning, Data Management |
| | User can add non-phase/protocol events (user defined) to the calendar anywhere | Data Management |
| | User can view images associated with phases | Data Management |
| | User can browse the .GAL file along with image and filter paper information | Data Management |
| | User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density | Data Management |
| | User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery | Data Management |
| | When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown | Data Management |
| | Application should allow for details of flushes to be seen/accounted for | Data Management |
| | The application should archive (and make available) the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts | Data Management |
| | Users should be able to download instrument logs and images and the GUI will parse out the following events:
* Track deployments of contextual sensors (sub-deployments of ESP)
* Collection of contextual sensor data (with capability to view/work with data) 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time | Data Management, State Visualization |
| | Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power | State Visualization |
| | Users can visualize the current state of the instrument | State Visualization |
| | Users can scroll back in time and visualize instrument state at the various points in time | State Visualization |

h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Glossary]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
# [01/11/2012 *GUI Update and Planning Meeting*|2011_01_12]
{panel}
{column}
{section}
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process.

h3. Requirements
|| Number || Requirement || Goal ||
| | User can define missions by specifying phases | Planning |
| | User can specify and adjust phase start times | Planning |
| | User can also specify a time to wait between events instead of a specific start time | Planning |
| | User can set mission start and end times that are not associated with a phase/protocol | Planning |
| | User can specify comments associated with missions that are printed at the top of the mission script | Planning |
| | After planning, application should generate mission script, puck loads, and reagent volumes | Planning |
| | User can add comments to a phase that will be generated in the script | Planning |
| | Users can add/delete/edit protocol runs and phases | Planning |
| | Users can add/delete/edit consumables | Planning |
| | Users can schedule Kills (end purges) or disable kills | Planning |
| | Users can define generic events and what script will actually be added to the master script (if needed) | Planning |
| | Mission plan generation will include a puck loading list | Planning |
| | User can associate external files with events (excel spreadsheet, documents, etc.) | Planning, Data Management |
| | Tide and phase information will be available | Planning, Data Management |
| | Application will list sample volumes with protocol run | Planning, Data Management |
| | User can add non-phase/protocol events (user defined) to the calendar anywhere | Data Management |
| | User can view images associated with phases | Data Management |
| | User can browse the .GAL file along with image and filter paper information | Data Management |
| | User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density | Data Management |
| | User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery | Data Management |
| | When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown | Data Management |
| | Application should allow for details of flushes to be seen/accounted for | Data Management |
| | The application should archive (and make available) the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts | Data Management |
| | Users should be able to download instrument logs and images and the GUI will parse out the following events:
* Track deployments of contextual sensors (sub-deployments of ESP)
* Collection of contextual sensor data (with capability to view/work with data) 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time | Data Management, State Visualization |
| | Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power | State Visualization |
| | Users can visualize the current state of the instrument | State Visualization |
| | Users can scroll back in time and visualize instrument state at the various points in time | State Visualization |

h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Glossary]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
# [01/11/2012 *GUI Update and Planning Meeting*|2011_01_12]
{panel}
{column}
{section}
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<property name="body"><![CDATA[In order to manage the data from multiple ESP deployments, a central data repository is required.  This repository needs the following functions:

h5. Requirement
# Provide access over many protocols (HTTP, WebDAV, FTP, SMB)
# Provide authentication and authorization to protect data from ESP deployments
# Provide notification mechanism to alert interested parties when files change and what changes were made.

h5. Design
# File Notification frameworks
## Node.js
### [Watch-tree|https://github.com/tafa/node-watch-tree]
### [log.io|http://logio.org] - For monitoring and send a single file, but might be useful.]]></property>
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<property name="body"><![CDATA[In order to manage the data from multiple ESP deployments, a central data repository is required.  This repository needs the following functions:

h5. Requirement
# Provide access over many protocols (HTTP, WebDAV, FTP, SMB)
# Provide authentication and authorization to protect data from ESP deployments
# Provide notification mechanism to alert interested parties when files change and what changes were made.

h5. Design
# File Notification frameworks
## Node.js
### [Watch-tree|https://github.com/tafa/node-watch-tree]
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|ESP Automated Image Analysis].

I'm working on a new method. Documentation is [here|ESP Automated Image Analysis 2]

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter 
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size. 
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h4. {panel:title=Administrative Items|BGcolor=blue|width=100%|borderWidth=4}




h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]
{panel}

{section}
{column:width=50%}

h4. {panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}

h4. {panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}

{column}
{section}]]></property>
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<property name="body"><![CDATA[h5. Goal

This meeting is to give an update and a walk through of the ESP GUI components, to get feedback and to put out a list of requests for things moving forward.

h5. Attendees

* Kevin Gomes
* Rich Schramm
* Brian Schlining

h5. Agenda

# Walk through of Planning/DM GUI
## [Deployment Diagram|ESPAPP:Design]
## [Starting the GUI|ESPAPP:2G ESP GUI Application]
## Setting preferences (Directory is local, repo is shared)
## Create new Instrument
## Create new deployment
## Show file pane, explain, then sync
## After sync, look at PCR files
## Parse log file
## Tabs
### ESP (dashboard connection)
### Planned
### Actual (show log file location with spanning lines)
### Images (show image, metadata, log entry)
### Samples (show log entry)
### Ancillary Data (Grab Gordon, CTD, ISUS, time window)
#### Zoom, print, save
### Files (open in browser, refresh, push to repo)
## Repository
# Walk through Dashboard
## Show work to date
### Use feedback (split and view)
## Talk about [Dashboard data protocol|ESPAPP:Real-Time ESP state update protocol framework]
# Walk through of Image Analysis
## Demo
## Show [wiki page|ESPAPP:ESP Image Analysis Application] for use
## Matlab

h5. Open issues

# Plan/Data
## Need way to determine exactly which contextual sensors on on ESP (CTD, ISUS, etc.)
## Need something in the log file that indicates when a DWSM inhale is done
# Dashboard
## Need to get data/simulator to start driving dashboard for development
## How do we then take this protocol and persist for playback (i.e. log file entries?)
# Image Analysis
## Got what he needs to keep going.

h5. Suggestions

# PCR Plots need separate axes for Temp and diode data.
# After adding assay, planned table does not updage]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|ESP Automated Image Analysis].

I'm working on a new method. Documentation is [here|ESP Automated Image Analysis 2]

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter 
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size. 
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|ESP Automated Image Analysis].

I'm working on a new method. Documentation is [here|ESP Automated Image Analysis 2]

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter 
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size. 
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h4. {panel:title=Administrative Items|BGcolor=blue|width=100%|borderWidth=4}




h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]
{panel}

{section}
{column:width=50%}

h4. {panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [Investigations into Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}

h4. {panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}

{column}
{section}]]></property>
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<property name="body"><![CDATA[h5. Goal

This meeting is to give an update and a walk through of the ESP GUI components, to get feedback and to put out a list of requests for things moving forward.

h5. Attendees

* Kevin Gomes
* Rich Schramm
* Brian Schlining

h5. Agenda

# Walk through of Planning/DM GUI
## [Deployment Diagram|ESPAPP:Design]
## [Starting the GUI|ESPAPP:2G ESP GUI Application]
## Setting preferences (Directory is local, repo is shared)
## Create new Instrument
## Create new deployment
## Show file pane, explain, then sync
## After sync, look at PCR files
## Parse log file
## Tabs
### ESP (dashboard connection)
### Planned
### Actual (show log file location with spanning lines)
### Images (show image, metadata, log entry)
### Samples (show log entry)
### Ancillary Data (Grab Gordon, CTD, ISUS, time window)
#### Zoom, print, save
### Files (open in browser, refresh, push to repo)
## Repository
# Walk through Dashboard
## Show work to date
### Use feedback (split and view)
## Talk about [Dashboard data protocol|ESPAPP:Real-Time ESP state update protocol framework]
# Walk through of Image Analysis
## Demo
## Show [wiki page|Investigations into Image Analysis Application] for use
## Matlab

h5. Open issues

# Plan/Data
## Need way to determine exactly which contextual sensors on on ESP (CTD, ISUS, etc.)
## Need something in the log file that indicates when a DWSM inhale is done
# Dashboard
## Need to get data/simulator to start driving dashboard for development
## How do we then take this protocol and persist for playback (i.e. log file entries?)
# Image Analysis
## Got what he needs to keep going.

h5. Suggestions

# PCR Plots need separate axes for Temp and diode data.
# After adding assay, planned table does not updage]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# [Extracting the intensities values from the filter image (_Data Extraction_)|#data]

See also: [Applying Fiducial Marks|#fiducials]

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}

h1. {anchor:data}Data Extraction

Without being able to align the filter image with the GAL points, it's impossible to:
# Associate a spot with it's content
# Accurately and reliable extract all spots of interest.

Here's a few examples of just trying to extract spots from an image:
{info:title=The Good}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_3-40s.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1.tif.png!
{info}
{info:title=The Bad}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-40s.tif.png!
{info}
{info:title=The Ugly}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}

h1. Summary

The only hurdle that needs to be overcome at this point is [pattern matching/image registration|#matching]

Here are the signficant hurdles for _pattern matching/image regsitration_:
# Reliably extracting spots from the filter image
#* In my test images, I was only able to extract all spots in one image using thresholding techniques.
#* Another technique to try would be edge detection. This may be problematic in noisier images though. 
# Dealing with symmetry in the spot layout, this confounds most image registration techniques.
#* It would be great if I could get some *key spots* that I can reliably detect and differentiate from the other spots. For example, 2 spots that are near the edge of the disk. If I could extract those then, I would be able to easily register the GAL file with the image. As an example, look at the image above an notice the single spot near the edge of the disk. If we had 2 of those on that image it would make my life much simpler!! ;-) ALthough in order to use those I would need be able to extract the same 2 spots from the GAL file.


h1. Applying Fiducial Marks for Image Analysis

If the ESP arrays had distinct fiducial marks it should be possible to locate these marks and use them for scaling and rotation of the GAL to match the array image. Ideally these fiducial's should be either the closest points to the center of mass of the or the farthest points from the center of mass.

h2. {anchor:fiducials}Applying Fiducials. 
* During analysis we extract the spots that are visible using a thresholding technique. This give an image like this: 
!fitler_3_aoi_masked.png!
* From this mask we can calculate a center of mass of the image. (The blue dot represents the center of mass) 
!filter_3-center-of-mass.png!
* To easily locate fiducial it would be best if they were either the points nearest the center-of-mass or farthest from it. The red dots in the images below represent notional fiducial points.
** Example of points nearest COM: 
!filter_3_center_fiducial.png!
** Example of points farthest from COM: 
!filter_3-distal_fiducial.png!




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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began?? and ended ~ week later when pump tore from piling.

*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).
Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays
Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

MELO used was #300034012090780

location reported by MELO was-\- &nbsp; 33.4865 \-118.51285

*March 20*\--lost comms

*March 21*\--re-established comms and think problem in E/M cable.

*March 22*\--lost comms

*April 3*\--small boat to buoy to test E/M cable

*April 8*\--'rescue' mission. Swapped E/M cables and repositioned in slightly deeper water, at 33.48504 \-118.50988

water depth 175m.&nbsp; top of can 10.9m

*RECOVERY--see below*

h4. {color:#ff00cc}ECOHAB--S. California{color}

*April 1*\--Instruments deployed

&nbsp;MOE--inshore at 33.60779 \-118.01877 with ISUS

Melo was 300234060014550

avg can depth \~9m
\\

&nbsp;Bruce--offshore at 33.58609 \-118.03686

Melo was 300234060016190

avg can depth \~19.5m

*~ April 9* lost communication with Bruce.&nbsp;

*April 15*\--Rescue mission w/Nerissa found 'hung' modem.&nbsp; Power cycled and checked cables on deck.&nbsp; Re-deployed in nearby spot.&nbsp; Divers (Kim R. & George M) measured 17.7m to top of can, 25.3 m to master link.

*RECOVERY*\--Plan was to pull ECOHAB April 30 with LBA0P divers off Nerissa, Catalina with Wrigley divers off Yellowfin May 1.&nbsp;&nbsp; April 30 had horrible Santa Ana winds; motored offshore to Bruce, and too rough.&nbsp; Cancelled entire day.&nbsp; Would try next day as winds supposed to die.&nbsp; Met at 5am and decided to cancel again, as winds were still blowing.&nbsp; Drove to Long Beach, and no wind up there. Salvaged that day by rounding up crew and wrigley divers after initially cancelling and heading over about noon.&nbsp; During that time, Dennis (skipper of Yellowfin) agreed to go the next day (Friday) to retrieve the two ECOHAB instruments.&nbsp; Eric Reinecker came down from MBARI, joining Jim Citanovich from SCMI and we retrieved Mack and Bruce.&nbsp; Back at SCMI around 1pm.&nbsp; Flatbed loaded by 4:30.&nbsp; Returned to MBARI next day (Saturday).

h4. {color:#ff00cc}Sulfur Cycling (Moran)--Monterey Bay{color}

*Sep 15*\--Instrument deployed

&nbsp;ESP-Gordon--at 36.83113 \-121.91114&nbsp; (M0) with ISUS and CTD.&nbsp; Forgot to start Melo (did it next day).&nbsp; Running archive-only mission, ended up deeper than we had hoped (~12m instead of 7-10m).

Sep 18--Went out in Paragon w/ 2 divers (Eric R & Lisa Z.).&nbsp; Pulled \~0.5mi toward M0.&nbsp; Now at 36.83480 \-121.89800 at 5-8m.&nbsp; Sampling has resumed. ]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# CVS client
# gcc
# yacc

h3. Steps to build and run

# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:
{code}
cvs checkout ESP/gen2/software
{code}
# &nbsp; (or if you want a branch like GUI2 (with head for anything not on branch \-f )
{code}
cvs checkout -f -r GUI2 ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.
{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This will populate the patch directory with the ruby source files without overwriting the patches.
# Now run configure.
{code}
./configure
{code}
# Now run make.
{code}
make
{code}
# If all goes well, ruby will have built and you can install by running this as 'root'.
{code}
make install
{code}
# After that, ruby should be ready to go and if you type
{code}
ruby --version
{code}
You should see something like:
{code}
ruby 1.6.8-mbari7/0x4770 (2009-1-19) [i686-linux]
{code}
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] -- first discussion of adaptive sampling strategies
# Mar 3 -- CMORE Hawaii
# [Mar 10]
# [Mar 17]
# [Mar 24]]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS]]></property>
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<property name="body"><![CDATA[h2. Quotes

* Sphere casting [(Wah Chang)|^Wah Chang quote MBARI 60200 11-14 C5.pdf]
* Machining
** [Tapemation|^Tapemation quote MBARI 4K Hemi.doc]
** Hanard Machine (sent for quote 11-15-07 --> [negative response])]]></property>
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<property name="body"><![CDATA[h3. Meeting Held?&nbsp;

Birch at NASA review.&nbsp;

h3. Tech Transfer


h3. Deployment


h3. MFB


h3. Software


h3. Sphere and 4K DWSMS


h3. GUI Development]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2019Feb08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# CVS client
# gcc
# yacc

h3. Steps to build and run

# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:
{code}
cvs checkout ESP/gen2/software
{code}
# &nbsp; (or if you want a branch like GUI2 (with head for anything not on branch \-f )
{code}
cvs checkout -f -r GUI2 ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.
{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This will populate the patch directory with the ruby source files without overwriting the patches.
# Now run configure.
{code}
./configure
{code}
# Now run make.
{code}
make
{code}
# If all goes well, ruby will have built and you can install by running this as 'root'.
{code}
make install
{code}
# After that, ruby should be ready to go and if you type
{code}
ruby --version
{code}
You should see something like:
{code}
ruby 1.6.8-mbari7/0x4770 (2009-1-19) [i686-linux]
{code}
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username]]></property>
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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* Middle of September; Japanese visitor to work on MFB.
* End of Sept for \~3 months;&nbsp; Allison Haywood (New Zealand) to work on a core.
* October deployment:
** Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs).
** there are enough ISUS's for deployment;&nbsp; must test all.

h3. Machine Builds

* Gripper boards are out for fabrications
* Puck sensor boards (10 made) have been modified and Scott is testing on GG in the fridge.&nbsp; Preliminary results look good at ambient (+/\- 1 degree difference from ambient; off 3 degrees at 5d C).
* Mack and Bruce being used (today) by SC group.&nbsp; Should be ready for October deployment with a simple reagent refill.
* Boards:
** 50 Dwarf / 10 Sleepy / 50 R-valve boards are in.&nbsp; Each needs a QC checkout which {color:#0000ff}{*}Dick{*}{color} started on 20Aug2008.
* Much discussion on the number of boards and the NEXT round of builds; could/should we do a board/camera redesign?
* Wiring harnesses are in and QC'd.&nbsp; Many assembled into their 'super-harnesses'.
* Still waiting on small machine parts from El Camino
* Installation of tubing on Moe is next; {color:#ff0000}should take 1 week{color}.&nbsp; Still need to mount AIV on Moe, which was originally scavenged for Neo.&nbsp; {color:#0000ff}{*}Cheri{*}{color} predicts {color:#ff0000}3-4 weeks{color} before Science gets Moe for check-out.
* {color:#0000ff}{*}Cheri{*}{color} will get Mike going on the small hand pieces for Moe's manipulator.

Rough calculations on Mooring Cost:

&nbsp;&nbsp;  Materials/Radios/machined parts/cables/bungee/all parts == $50K + 2 mo's labor

h3. &nbsp;MFB

* Grill is working\! as are PCR scripts
* SPE script is close but syringe continues to have trajectory errors.&nbsp; Much discussion on how to address.&nbsp; Decision to run overnight to 'break-in' and see if sticktion issues are still a problem at slow speeds tomorrow.&nbsp; If that doesn't fix it, we can either gear down motor (but this has problems; fast moves would be slow, mechanical advantage makes it more likely to break something if valve gets stuck), or find a more compatible plunger/barrel combination.
* Stand-alone power boards not yet begun ({color:#0000ff}{*}Scott{*}{color}).
* Go/no-go on PCR for October deployment depends on how PCR does in cold.
* Mechanical changes for NEO to accomodate grill are finished, but scripts need testing.&nbsp; PCR/core group will meet today at 2:00pm to discuss integration.

h3. Software


* Antenna at Novin's (Sunset Dr, Watsonville).&nbsp; Brent and Wayne going out today to scout and sign agreement w/ homowner.
* DWSM code
** starting to test limit-switches; development of this code is on-going
** DWSM code is to a state where we could start testing if we had an instrument.
* Brent mentioned that if the new puck thermal-sensor is super-accurate, then maybe no calibration is needed (the preferred method).&nbsp; Perhaps insulating sensor may add to it's stability/accuracy.
* Brent fixed a core bug.&nbsp; The handling of background threads by using the 'stop' command now works.

h3. DWSM

* &nbsp;Doug spoke with El Camino regarding DWSM parts.&nbsp; Bell housing should finish this week, anodized next week.
* No DMO discussion yet on weight balance/elevator design
* Min-Cons to be ordered by Scott;&nbsp; may take awhile because made of titanium (or 'ti-dized')
* Pressure testing;&nbsp; We do NOT need to got to 4K, thus we will send/take sphere to Port Hueneme for testing.


NEXT WEEK:

&nbsp;Bring Calendar for deployment planning

Must test new syringes that arrived yesterday&nbsp;]]></property>
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<property name="body"><![CDATA[h2. &nbsp;

We currently (12-2012) have three Melo trackers.

{color:#006600}The Melo is the 'watch-circle' warning transponder for surface moorings.{color}
\\

IMEI numbers:

h3. *300034012090780&nbsp; (purchased June, 2011)*


User's Manuals
# [Quick Start Guide v1.2|^Xeos_Melo_manual-1.pdf|quick start]
# [User Manual v1.5|^Xeos_Melo_manual-2.pdf|Full Manual]
# [Watch Circle Console User Manual v2.1|^Xeos_Melo_manual-3.pdf|watch circle]\\ \\

h3. \\


h3.


h3.


h3. 300234060016190&nbsp; (serial # 122)&nbsp;&nbsp; (both purchased Dec, 2012)



h3. 300231060014550 (serial # 123)


h3. &nbsp;]]></property>
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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* Middle of September; Japanese visitor to work on MFB.
* End of Sept for \~3 months;&nbsp; Allison Haywood (New Zealand) to work on a core.
* October deployment:
** Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs).&nbsp;

h3. Machine Builds

* Gripper boards are out for fabrications
* Puck sensor boards (10 made) have been modified and Scott is testing on GG in the fridge.&nbsp; Preliminary results look good at ambient (+/\- 1 degree difference from ambient; off 3 degrees at 5d C).
* Mack and Bruce being used (today) by SC group.&nbsp; Should be ready for October deployment with a simple reagent refill.
* Boards:
** 50 Dwarf / 10 Sleepy / 50 R-valve boards are in.&nbsp; Each needs a QC checkout which {color:#0000ff}{*}Dick{*}{color} started on 20Aug2008.
* Much discussion on the number of boards and the NEXT round of builds; could/should we do a board/camera redesign?
* Wiring harnesses are in and QC'd.&nbsp; Many assembled into their 'super-harnesses'.
* Still waiting on small machine parts from El Camino
* Installation of tubing on Moe is next; {color:#ff0000}should take 1 week{color}.&nbsp; Still need to mount AIV on Moe, which was originally scavenged for Neo.&nbsp; {color:#0000ff}{*}Cheri{*}{color} predicts {color:#ff0000}3-4 weeks{color} before Science gets Moe for check-out.
* {color:#0000ff}{*}Cheri{*}{color} will get Mike going on the small hand pieces for Moe's manipulator.

Rough calculations on Mooring Cost:

&nbsp;&nbsp;  Materials/Radios/machined parts/cables/bungee/all parts == $50K + 2 mo's labor

h3. &nbsp;MFB
\\
* Grill is working\! as are PCR scripts
* SPE script is close but syringe continues to have trajectory errors.&nbsp; Much discussion on how to address.&nbsp; Decision to run overnight to 'break-in' and see if sticktion issues are still a problem at slow speeds tomorrow.&nbsp; If that doesn't fix it, we can either gear down motor (but this has problems; fast moves would be slow, mechanical advantage makes it more likely to break something if valve gets stuck), or find a more compatible plunger/barrel combination.
* Stand-alone power boards not yet begun ({color:#0000ff}{*}Scott{*}{color}).


MFB
•&nbsp;&nbsp; &nbsp;Current grill status.
•&nbsp;&nbsp; &nbsp;PCR decision for October deployment.
•&nbsp;&nbsp; &nbsp;Chris' test schedule for joining PCR to ESP.
•&nbsp;&nbsp; &nbsp;Status for the MBARI populated power boards

Software
•&nbsp;&nbsp; &nbsp;Antenna update
•&nbsp;&nbsp; &nbsp;DWSM code update
•&nbsp;&nbsp; &nbsp;Kevin G.---update on mission planning/machine state

DWSM
•&nbsp;&nbsp; &nbsp;Bell housings.&nbsp; 3 week prediction on 7 Aug. Status?
•&nbsp;&nbsp; &nbsp;Informal discussion with DMO about weight balance?
•&nbsp;&nbsp; &nbsp;COTS parts:&nbsp; mini-cons, swageloc, connectors/cables status.
•&nbsp;&nbsp; &nbsp;Pressure testing quotes.

Other Items

•&nbsp;&nbsp; &nbsp;Syringe update]]></property>
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<property name="body"><![CDATA[h2. IMEI number for the Melo tracker:


h1. *300034012090780*

{color:#006600}The Melo is the 'watch-circle' warning transponder for surface moorings.&nbsp;{color}


User's Manuals
# [Quick Start Guide v1.2|^Xeos_Melo_manual-1.pdf|quick start]
# [User Manual v1.5|^Xeos_Melo_manual-2.pdf|Full Manual]
# [Watch Circle Console User Manual v2.1|^Xeos_Melo_manual-3.pdf|watch circle]]]></property>
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</property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]]]></property>
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<property name="body"><![CDATA[h2. &nbsp;

We currently (12-2012) have three Melo trackers.

{color:#006600}The Melo is the 'watch-circle' warning transponder for surface moorings.{color}\\

IMEI numbers:

h3. *300034012090780&nbsp; (purchased June, 2011)*

User's Manuals
# [Quick Start Guide v1.2|^Xeos_Melo_manual-1.pdf|quick start]
# [User Manual v1.5|^Melo_User_Manual_watch_circle_V1.5.pdf|Full Manual]
# [Watch Circle Console User Manual v2.1|^Xeos_Melo_manual-3.pdf|watch circle]\\
\\

h3. \\


h3.


h3.


h3. 300234060016190&nbsp; (serial # 122)&nbsp;&nbsp; (both purchased Dec, 2012)


h3. 300231060014550 (serial # 123)


h3. &nbsp;]]></property>
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<property name="body"><![CDATA[{mockup:InstrumentState|1}

As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|1}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|1}

{mockup:EventDetails|1}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

Mockup of instrument state

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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|1}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|1}

{mockup:EventDetails|1}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

Mockup of instrument state

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<property name="body"><![CDATA[Present:&nbsp; Jim, Bill, Brent, Doug, Scott, Roman


h3. JdF Preparations

* Wand design continues.&nbsp; Doug has ideas for a simple wand/heat exchanger.&nbsp; Will talk to pilots about their wishes.
* Scott discovered that failed encoder in HPP seems to be from vibration breaking wires potted in soft silicon.&nbsp; He's ordered 3 more encoders, and we are have a brace made that will hopefully minimize shaking of the encoder.&nbsp; Doug suggested doing some math on maximum accelerations might explain wires breaking.&nbsp; Could be oil degrading silicon.&nbsp; Still investigating.&nbsp;
* New torque nuts&nbsp; (SuperNuts) have arrived.&nbsp;

h3. &nbsp;Adaptive Sampling and M0 Deployment&nbsp; (MOE)

* MOE deploys in one week.&nbsp; Arrays and PCR looking beautiful, but implementing adaptive sampling causing difficulties.
* Porting Yanwu's code from Matlab to Ruby more involved than initially thought.&nbsp; This adaptive sampling code will not make it on this deployment.
* Revert to simple event detection (triggering on nitrate).&nbsp; First iteration of this code caused major Ruby crashes.&nbsp; This code has been changed and is being tested right now.&nbsp; We must make it through 3 runs to give it stamp of approval.&nbsp; We will know by noon if we continue with this code or revert back to old ESP code without event triggering.&nbsp; Much thanks to Chris P and Brent for hammering on this....
* 'air-battery' containers are at bottom of test tank.&nbsp; Paul C. working on mounting.&nbsp; They should be ready.&nbsp;

h3. WHOI Deployment

* &nbsp;Still haven't pulled connector off 3rd E/M cable;&nbsp; one bolt is stuck.&nbsp; If it breaks, cone is ruined.&nbsp; Roman working this.
* Shipping option has been selected.&nbsp; Temp controlled truck arrives for loading April 1.&nbsp; Will arrive at WHOI April 7 or 8 into Roman's waiting hands (he fly's out the 6th).&nbsp; This shipping option costing \~$7K.&nbsp; We will need a place to store our totes at WHOI (no van is being left behind).
* Doug ordered cushioning material for ESP can.&nbsp; Will get Greg Voogd to help build a 'floor' that will sit in palletainer.
* Roman has sent out paperwork for He leak detector rental ($700/week).&nbsp; They will ship it to WHOI; we'll have for 3 weeks.&nbsp; WHOI has He and N2 and regulators.
* Deployment plan:
** Leave WHOI as early as possible Tuesday, April 19.&nbsp; Arrive at NH Science center dock that evening.&nbsp; Sleep on boat.&nbsp; Early AM, April 20, divers arrive, get on boat.&nbsp; Motor to site and deploy.&nbsp; Do some water casts around ESP while we make sure it's working.&nbsp; Return divers to dock and continue water sampling transect.&nbsp; Begin return to WHOI early

h3. G3 Development

* Spoke with Jim Bellingham about a 2foot section on front of LRAUV.&nbsp; He suggests we do a quick remodel with his fluid dynamics guy.&nbsp; Email introduction has been made.&nbsp; He has also thought of the possibility of scaling the AUV to be bigger....sigh. ]]></property>
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<property name="body"><![CDATA[{mockup:InstrumentStateSelect|1}

{mockup:ConsumedResources|1}

{mockup:DeploymentPlannedResources|1}

{mockup:EventDetails|1}

{mockup:MouseOverEvent|1}

As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|1}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

Mockup with mouse over

Mockup with detail box

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

The user can also select a tab which shows the planned resources for the selected deployment.

The user can also select a tab which shows the consumed resources to date.

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

Mockup of menu

Mockup of instrument state

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<property name="body"><![CDATA[{mockup:ConsumedResources|1}

{mockup:DeploymentPlannedResources|1}

{mockup:EventDetails|1}

{mockup:MouseOverEvent|1}

As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|1}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

Mockup with mouse over

Mockup with detail box

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

The user can also select a tab which shows the planned resources for the selected deployment.

The user can also select a tab which shows the consumed resources to date.

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

Mockup of menu

Mockup of instrument state

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<property name="body"><![CDATA[{mockup:DeploymentPlannedResources|1}

{mockup:EventDetails|1}

{mockup:MouseOverEvent|1}

As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|1}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

Mockup with mouse over

Mockup with detail box

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

The user can also select a tab which shows the planned resources for the selected deployment.

The user can also select a tab which shows the consumed resources to date.

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

Mockup of menu

Mockup of instrument state

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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] -- first discussion of adaptive sampling strategies
# Mar 3 -- CMORE Hawaii
# [Mar 10]
# [Mar 17]]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://predator.shore.mbari.org/esp_gui/launch.jnlp]

h3. Project Documentation:

h3. Other Documents
# [Documents|Documents Related to GUI Component]
# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
## [ESP GUI Demo and Questions|2007_09_05]
## [Follow up meeting on Resources and Consumables|2008_01_08]
## [Mock Mission Planning Meeting|2008_03_11]
# [Presentations|ProjectPresentations]
# [Data Model]
# [Developer Documentation]

h3. Bug Tracking
# [JIRA Issue Tracker|http://oceana.shore.mbari.org:8082/browse/ESPII]

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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|6}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:Top Level|7}

After learning about the instrument, I might want to know more about the deployments (past, present and future).
# Select deployment from list, or from calendar which would then provide information about the individual deployments of the ESP.
## Name, geospatial location
## View list of phases
## View list of any events (like from log file or user entered)
## View comments about the deployment
## View images from phases
## View array maps from phases
## Planned resources (amounts, sizes, etc.)
## Resources consumed (for in process/previous).

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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|7}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.

After learning about the instrument, I might want to know more about the deployments (past, present and future).
# Select deployment from list, or from calendar which would then provide information about the individual deployments of the ESP.
## Name, geospatial location
## View list of phases
## View list of any events (like from log file or user entered)
## View comments about the deployment
## View images from phases
## View array maps from phases
## Planned resources (amounts, sizes, etc.)
## Resources consumed (for in process/previous).

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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|7}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:Top Level|7}

After learning about the instrument, I might want to know more about the deployments (past, present and future).
# Select deployment from list, or from calendar which would then provide information about the individual deployments of the ESP.
## Name, geospatial location
## View list of phases
## View list of any events (like from log file or user entered)
## View comments about the deployment
## View images from phases
## View array maps from phases
## Planned resources (amounts, sizes, etc.)
## Resources consumed (for in process/previous).

]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).
# Logical next step would be for the user to explore the information presented:
## Information about each ESP
### Serial Number
### Picture?
## Information about the individual deployments of the ESP.
### Name, geospatial location
### View list of phases
### View list of any events (like from log file or user entered)
### View comments about the deployment
### View images from phases
### View array maps from phases
### Planned resources (amounts, sizes, etc.)
### Resources consumed (for in process/previous).

Then I decide I want to examine one particular instrument.  I select which instrument I am interested in and then can get more details on the deployments (past, current, and planned) by selecting the various deployments.

As a first cut at a GUI, a mockup was created and we just put tabs in to differentiate between the different groups of functionality.  The view shown here is from the mission planning perspective.  You can see that even though the components are differentiated, they have spilled over into each other.  In other words from the planning GUI, you can see data.
{mockup:Top Level|6}]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|7}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:Top Level|6}

After learning about the instrument, I might want to know more about the deployments (past, present and future).
# Select deployment from list, or from calendar which would then provide information about the individual deployments of the ESP.
## Name, geospatial location
## View list of phases
## View list of any events (like from log file or user entered)
## View comments about the deployment
## View images from phases
## View array maps from phases
## Planned resources (amounts, sizes, etc.)
## Resources consumed (for in process/previous).

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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|6}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:Top Level|6}

After learning about the instrument, I might want to know more about the deployments (past, present and future).
# Select deployment from list, or from calendar which would then provide information about the individual deployments of the ESP.
## Name, geospatial location
## View list of phases
## View list of any events (like from log file or user entered)
## View comments about the deployment
## View images from phases
## View array maps from phases
## Planned resources (amounts, sizes, etc.)
## Resources consumed (for in process/previous).

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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).
# Logical next step would be for the user to explore the information presented:
## Information about each ESP
### Serial Number
### Picture?
## Information about the individual deployments of the ESP.
### Name, geospatial location
### View list of phases
### View list of any events (like from log file or user entered)
### View comments about the deployment
### View images from phases
### View array maps from phases
### Planned resources (amounts, sizes, etc.)
### Resources consumed (for in process/previous).

Then I decide I want to examine one particular instrument.  I select which instrument I am interested in and then can get more details on the deployments (past, current, and planned) by selecting the various deployments.

As a first cut at a GUI, a mockup was created and we just put tabs in to differentiate between the different groups of functionality.  The view shown here is from the mission planning perspective.  You can see that even though the components are differentiated, they have spilled over into each other.  In other words from the planning GUI, you can see data.
{mockup:Top Level|6}]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):

# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:

# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).
# Then I decide I want to examine one particular instrument.  I select which instrument I am interested in and then can get more details on the deployments (past, current, and planned) by selecting the various deployments.

As a first cut at a GUI, a mockup was created and we just put tabs in to differentiate between the different groups of functionality.  The view shown here is from the mission planning perspective.  You can see that even though the components are differentiated, they have spilled over into each other.  In other words from the planning GUI, you can see data.

{mockup:Top Level|6}
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).
# Logical next step would be for the user to explore the information presented:
## Information about each ESP
### Serial Number
### Picture?
## Information about the individual deployments of the ESP.
### Name, geospatial location
### View list of phases
### View list of any events (like from log file or user entered)
### View comments about the deployment
### View images from phases
### View array maps from phases
### Planned resources (amounts, sizes, etc.)
### Resources consumed (for in process/previous).

Then I decide I want to examine one particular instrument.  I select which instrument I am interested in and then can get more details on the deployments (past, current, and planned) by selecting the various deployments.

As a first cut at a GUI, a mockup was created and we just put tabs in to differentiate between the different groups of functionality.  The view shown here is from the mission planning perspective.  You can see that even though the components are differentiated, they have spilled over into each other.  In other words from the planning GUI, you can see data.
{mockup:Top Level|5}]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] --Discussion of G3]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):

# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:

# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).
# Then I decide I want to examine one particular instrument.  I select which instrument I am interested in and then can get more details on the deployments (past, current, and planned) by selecting the various deployments.

As a first cut at a GUI, a mockup was created and we just put tabs in to differentiate between the different groups of functionality.  The view shown here is from the mission planning perspective.  You can see that even though the components are differentiated, they have spilled over into each other.  In other words from the planning GUI, you can see data.

{mockup:Top Level|5}
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|1}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

Mockup with mouse over

Mockup with detail box
# Event name
# Event time
# Event composition? (child events?)
# View comments about the deployment
# Associated images(if applicable) (HTTP linked to source)
# Array Map (if applicable) (HTTP linked to source)

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

The user can also select a tab which shows the planned resources for the selected deployment.

The user can also select a tab which shows the consumed resources to date.
To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

Mockup of menu

Mockup of instrument state

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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|1}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

Mockup with mouse over

Mockup with detail box

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

The user can also select a tab which shows the planned resources for the selected deployment.

The user can also select a tab which shows the consumed resources to date.

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

Mockup of menu

Mockup of instrument state

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<property name="body"><![CDATA[{mockup:MouseOverEvent|1}

As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|1}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

Mockup with mouse over

Mockup with detail box

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

The user can also select a tab which shows the planned resources for the selected deployment.

The user can also select a tab which shows the consumed resources to date.

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

Mockup of menu

Mockup of instrument state

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{mockup:MouseOverEvent|1}

As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|1}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

Mockup with mouse over

Mockup with detail box

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

The user can also select a tab which shows the planned resources for the selected deployment.

The user can also select a tab which shows the consumed resources to date.

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

Mockup of menu

Mockup of instrument state

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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|1}

After learning about the instrument, I might want to know more about the deployments (past, present and future).
# Select deployment from list, or from calendar which would then provide information about the individual deployments of the ESP.
## Name, geospatial location
## View list of phases
## View list of any events (like from log file or user entered)
## View comments about the deployment
## View images from phases
## View array maps from phases
## Planned resources (amounts, sizes, etc.)
## Resources consumed (for in process/previous).
{mockup:DeploymentSelect|1}

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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|1}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|1}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

Mockup with mouse over

Mockup with detail box
# Event name
# Event time
# Event composition? (child events?)
# View comments about the deployment
# Associated images(if applicable) (HTTP linked to source)
# Array Map (if applicable) (HTTP linked to source)

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

The user can also select a tab which shows the planned resources for the selected deployment.

The user can also select a tab which shows the consumed resources to date.
To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

Mockup of menu

Mockup of instrument state

]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|10}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.

After learning about the instrument, I might want to know more about the deployments (past, present and future).
# Select deployment from list, or from calendar which would then provide information about the individual deployments of the ESP.
## Name, geospatial location
## View list of phases
## View list of any events (like from log file or user entered)
## View comments about the deployment
## View images from phases
## View array maps from phases
## Planned resources (amounts, sizes, etc.)
## Resources consumed (for in process/previous).

]]></property>
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<property name="body"><![CDATA[{mockup:InstrumentSelect|1}

As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|10}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.

After learning about the instrument, I might want to know more about the deployments (past, present and future).
# Select deployment from list, or from calendar which would then provide information about the individual deployments of the ESP.
## Name, geospatial location
## View list of phases
## View list of any events (like from log file or user entered)
## View comments about the deployment
## View images from phases
## View array maps from phases
## Planned resources (amounts, sizes, etc.)
## Resources consumed (for in process/previous).

]]></property>
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<property name="body"><![CDATA[
As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|1}

After learning about the instrument, I might want to know more about the deployments (past, present and future).
# Select deployment from list, or from calendar which would then provide information about the individual deployments of the ESP.
## Name, geospatial location
## View list of phases
## View list of any events (like from log file or user entered)
## View comments about the deployment
## View images from phases
## View array maps from phases
## Planned resources (amounts, sizes, etc.)
## Resources consumed (for in process/previous).

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<property name="body"><![CDATA[{mockup:DeploymentSelect|1}


As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|1}

After learning about the instrument, I might want to know more about the deployments (past, present and future).
# Select deployment from list, or from calendar which would then provide information about the individual deployments of the ESP.
## Name, geospatial location
## View list of phases
## View list of any events (like from log file or user entered)
## View comments about the deployment
## View images from phases
## View array maps from phases
## Planned resources (amounts, sizes, etc.)
## Resources consumed (for in process/previous).

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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|8}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.

After learning about the instrument, I might want to know more about the deployments (past, present and future).
# Select deployment from list, or from calendar which would then provide information about the individual deployments of the ESP.
## Name, geospatial location
## View list of phases
## View list of any events (like from log file or user entered)
## View comments about the deployment
## View images from phases
## View array maps from phases
## Planned resources (amounts, sizes, etc.)
## Resources consumed (for in process/previous).

]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|9}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.

After learning about the instrument, I might want to know more about the deployments (past, present and future).
# Select deployment from list, or from calendar which would then provide information about the individual deployments of the ESP.
## Name, geospatial location
## View list of phases
## View list of any events (like from log file or user entered)
## View comments about the deployment
## View images from phases
## View array maps from phases
## Planned resources (amounts, sizes, etc.)
## Resources consumed (for in process/previous).

]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Bill, Elif, Brent, Chris P, Doug, Scott, Roman, Chris S.

h3. JdF Preparations

* Parts for wand and temperature sensor are either ordered or have arrived.&nbsp; Build and design of wand continues.&nbsp; Temp probe tips have arrived and have been pressure-tested.
* encoder in HPP seems to have failed (again).&nbsp; Either because oil gets on it or some unknown electrical issue.&nbsp; Scott working on this problem.
* Doug awaiting new nuts that relieve us of having to use special torque wrench to get to recommended torque when closing DWSM for high-pressure testing.&nbsp; These should arrive tomorrow or Monday.&nbsp; Then high-pressure testing should commence (if HPP fixed).
* Bill has a straw man crew list for JdF [here|^Juan de Fuca Science Crew List.doc]

h3. &nbsp;Adaptive Sampling and M0 Deployment&nbsp; (MOE)

* Ran 1st integrated run yesterday; water very stinky and PCR was inhibited, but mechanically ran fine.&nbsp; Array was good.&nbsp; Starting 2nd sample tonight.&nbsp; We want 3 good runs in a row to say it passes qualification.
* Will set up MOE with ISUS and CTD to begin lab testing of adaptive sampling on Monday.&nbsp; John R. taking care of the ISUS cleaning/preparation.
* Brent to receive Yanwu's code on Friday and might work on over weekend to get it into 'ESP-speak'
* Deployment has been moved UP to March 31.&nbsp; Although this makes for slightly longer deployment we thing no problem with power and # of samples.
* We are using the 'air-battery' containers for this deployment (not orange boxes).&nbsp; Almost finished, but must check who is making brackets for mounting these.

h3. WHOI Deployment

* &nbsp;Currently we have 3 E/M cables.&nbsp; in meters: 15a, 15b and 20.&nbsp; The 20m did not ohm, and we found water and corrosion in one connector.&nbsp; That has been cleaned and 'resealed' with lots of silicone grease.&nbsp; 15b passed the ohm test, but showed some funky readings (i.e., not perfect).&nbsp; 15a works, and debate was whether to pull it apart.&nbsp; Decision was yes, pull, inspect, and grease.&nbsp; We will use this shortest cable (15a) for WHOI since there's lots of activity in the area of the mooring (lobster pots).
* WHOI to provide their own batteries, but we should test their polarities.&nbsp; Also make sure they have an interface cable if we're doing a hot-swap.
* Brent heading to WHOI on March 27.&nbsp; 2 days setting up shore-station, and 3 days assisting EOM/McLane in getting ESP to talk up their gumby.
* Roman working with Doug to see if we can rent a He leak detector while at WHOI.
* Various shipping options are being explored with the help of Teresa Cardoza.

h3. G3 Development

* We will have a G3 meeting next Tuesday at the normal ESP Science meeting to discuss some discussions that Doug/Scott have had. ]]></property>
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<property name="body"><![CDATA[15m EM cable Float Locations
Float number     Distance from Bale Flange(meters)
1                0.9
2                1.25
3                1.62
4                2.03
5                2.66
6                3.23
7                3.90
8                4.57
9                5.36
10               6.03
11               6.79
12               7.49
13               8.20
14               9.04

One of the cable measures from flange to flange 13.92m]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 17 July 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics_worksheet_17JulFeb08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]

h3. Project Documentation:
# [Requirements Gathering|Documents Related to GUI Component]
# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
## [ESP GUI Demo and Questions|2007_09_05]
## [Follow up meeting on Resources and Consumables|2008_01_08]
## [Mock Mission Planning Meeting|2008_03_11]
# [Presentations|ProjectPresentations]
# [Data Model]
# [Developer Documentation]

h3. Bug Tracking
# [JIRA Issue Tracker|https://oceana.mbari.org/jira/browse/ESPII]

]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  --CMORE Hawaii
# Mar 8  --ad hoc mtg
# [Mar 15]]]></property>
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</property>
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<property name="body"><![CDATA[# [Requirements]
# [Terminology]
# [Outstanding Questions]
# [Assumptions]
]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]

h3. Project Documentation:

h3. Other Documents
# [Documents|Documents Related to GUI Component]
# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
## [ESP GUI Demo and Questions|2007_09_05]
## [Follow up meeting on Resources and Consumables|2008_01_08]
## [Mock Mission Planning Meeting|2008_03_11]
# [Presentations|ProjectPresentations]
# [Data Model]
# [Developer Documentation]

h3. Bug Tracking
# [JIRA Issue Tracker|https://oceana.mbari.org/jira/browse/ESPII]

]]></property>
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<property name="body"><![CDATA[# Meeting Notes
## [PDR Notes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
## [ESP GUI Demo and Questions|2007_09_05]
## [Follow up meeting on Resources and Consumables|2008_01_08]
## [Mock Mission Planning Meeting|2008_03_11]
# [Requirements]
# [Terminology]
# [Outstanding Questions]
# [Assumptions]
]]></property>
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h3. GUI Product
# [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]

h3. Project Documentation:
# [Requirements Gathering|Documents Related to GUI Component]
# [Presentations|ProjectPresentations]
# [Data Model]
# [Developer Documentation]

h3. Bug Tracking
# [JIRA Issue Tracker|https://oceana.mbari.org/jira/browse/ESPII]

]]></property>
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<property name="body"><![CDATA[# Meeting Notes
## [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
## [ESP GUI Demo and Questions|2007_09_05]
## [Follow up meeting on Resources and Consumables|2008_01_08]
## [Mock Mission Planning Meeting|2008_03_11]
# [Requirements]
# [Terminology]
# [Outstanding Questions]
# [Assumptions]
]]></property>
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<property name="body"><![CDATA[# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
## [ESP GUI Demo and Questions|2007_09_05]
## [Follow up meeting on Resources and Consumables|2008_01_08]
## [Mock Mission Planning Meeting|2008_03_11]
# [Requirements]
# [Terminology]
# [Outstanding Questions]
# [Assumptions]
]]></property>
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<property name="body"><![CDATA[h3. Meeting Notes
## [PDR Notes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
## [ESP GUI Demo and Questions|2007_09_05]
## [Follow up meeting on Resources and Consumables|2008_01_08]
## [Mock Mission Planning Meeting|2008_03_11]

h3. Requirements
# [Requirements]

h3. Supporting Documents
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
]]></property>
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<property name="body"><![CDATA[# Meeting Notes
## [PDR Notes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
## [ESP GUI Demo and Questions|2007_09_05]
## [Follow up meeting on Resources and Consumables|2008_01_08]
## [Mock Mission Planning Meeting|2008_03_11]
# [Requirements]
# [Terminology]
# [Outstanding Questions]
# [Assumptions]
]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] -- first discussion of adaptive sampling strategies
# Mar 3 -- CMORE Hawaii
# [Mar 10]]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]

h3. Project Documentation:
# [Requirements Gathering|Requirements Gathering Documentation]
# [Presentations|ProjectPresentations]
# [Data Model]
# [Developer Documentation]

h3. Bug Tracking
# [JIRA Issue Tracker|https://oceana.mbari.org/jira/browse/ESPII]

]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Bill, Elif, Brent, Chris P, Doug, Scott, Roman, Chris S.

h3. JdF Preparations

* Parts for wand and temperture sensor are either ordered or have arrived.&nbsp; Build and design of wand continues.
* encoder in HPP seems to have failed (again).&nbsp; Either because oil gets on it or some unknown electrical issue.&nbsp; Scott working on this problem.
* Doug awaiting new nuts that relieve us of having to use special torque wrench to get to recommended torque when closing DWSM for high-pressure testing.&nbsp; These should arrive tomorrow or Monday.&nbsp; Then high-pressure testing should commence (if HPP fixed).
* Bill has a straw man crew list for JdF [here|^Juan de Fuca Science Crew List.doc]
* &nbsp;

h3. &nbsp;Adaptive Sampling and M0 Deployment&nbsp; (MOE)

* Ran 1st integrated run yesterday; water very stinky and PCR was inhibited, but mechanically ran fine.&nbsp; Array was good.&nbsp; Starting 2nd sample tonight.&nbsp; We want 3 good runs in a row to say it passes qualification.
* Will set up MOE with ISUS and CTD to begin lab testing of adaptive sampling on Monday.&nbsp; John R. taking care of the ISUS cleaning/preparation.
* Brent to receive Yanwu's code on Friday and might work on over weekend to get it into 'ESP-speak'
* Deployment has been moved UP to March 31.&nbsp; Although this makes for slightly longer deployment we thing no problem with power and # of samples.&nbsp;

h3. M0 Spring Deployment

* Chris and Roman making excellent progress
** MOE will have reagents by end of today
** MFB gets mated on Monday
** QC tests next week
** Week of March 21 we'll test adaptive sampling
** Can on April 1
** Deploy April 7

* There was some discussion of the Zephyr also deploying another instrument at M0, using our cruise.&nbsp; Will check on this.

h3. &nbsp;WHOI Deployment

* &nbsp;All systems moving forward.&nbsp; Turner Calvis (?) is the guy to contact at UCONN regarding divers.&nbsp; Roman is on this.
* &nbsp;]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]

h3. Project Documentation:
# [Requirements Gathering|Requirements Gathering Documentation]
# [Design]
# [Presentations|ProjectPresentations]
# [Data Model]
# [Developer Documentation]
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]

]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Bill, Elif, Brent, Chris P, Doug, Scott, Roman, Chris S.

\\

h3.


h3. JdF Preparations

* Parts for wand and temperture sensor are either ordered or have arrived.&nbsp; Build and design of wand continues.
* encoder in HPP seems to have failed (again).&nbsp; Either because oil gets on it or some unknown electrical issue.&nbsp; Scott working on this problem.
* Doug awaiting new nuts that relieve us of having to use special torque wrench to get to recommended torque when closing DWSM for high-pressure testing.&nbsp; These should arrive tomorrow or Monday.&nbsp; Then high-pressure testing should commence (if HPP fixed).
* Bill has a straw man crew list for JdF [here|https://oceana.mbari.org/confluence/plugins/tinymce/wysiwyg-insertlink-draft-uploadfile.action#].
* &nbsp;

h3. &nbsp;Adaptive Sampling and M0 Deployment&nbsp; (MOE)

* Ran 1st integrated run yesterday; water very stinky and PCR was inhibited, but mechanically ran fine.&nbsp; Array was good.&nbsp; Starting 2nd sample tonight.&nbsp; We want 3 good runs in a row to say it passes qualification.
* Will set up MOE with ISUS and CTD to begin lab testing of adaptive sampling on Monday.&nbsp; John R. taking care of the ISUS cleaning/preparation.
* Brent to receive Yanwu's code on Friday and might work on over weekend to get it into 'ESP-speak'
* Deployment has been moved UP to March 31.&nbsp; Although this makes for slightly longer deployment we thing no problem with power and # of samples.&nbsp;

h3. M0 Spring Deployment

* Chris and Roman making excellent progress
** MOE will have reagents by end of today
** MFB gets mated on Monday
** QC tests next week
** Week of March 21 we'll test adaptive sampling
** Can on April 1
** Deploy April 7

* There was some discussion of the Zephyr also deploying another instrument at M0, using our cruise.&nbsp; Will check on this.

h3. &nbsp;WHOI Deployment

* &nbsp;All systems moving forward.&nbsp; Turner Calvis (?) is the guy to contact at UCONN regarding divers.&nbsp; Roman is on this.
* &nbsp;]]></property>
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<property name="body"><![CDATA[h3. Meeting Notes

# PDR Meeting (June 6, 2007)
## Attendees
### Rich Schramm
### Kevin Gomes
### Chris Scholin
### Doug Pargett
### Scott McLean
### Jim Birch
## Slides
## Demo Mockup
## WBS/Costs

]]></property>
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<property name="body"><![CDATA[re: cube/filter testing \-\- pure water should should be filtered to a standard spec (e.g. 0.1 or 0.2um) so we can get the most repeatable flow rates/bubble pt measurements as per industry standards for characterizing filters.
\\

For seawater samples, we should always include a standard lab bench equivalent (e.g., pressure driven or vacuum manifold) to compare both filtration efficiency and performance of downstream analyses.&nbsp; With such standard procedures, we will be better placed to evaluate G3 filter/upstream processing with seawater that will vary depending on when/where it's collected.]]></property>
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<property name="body"><![CDATA[{gliffy:name=volume margins|space=ESPAPP|page=ESP -- SURF Center Main Page|pageid=2162822|align=left|size=M}
h1. Welcome to the ESP - SURF Center


h3. {color:#009900}[ESP Logos]{color}


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h3. {color:#009900}[ESP Logos]{color}


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010]]></property>
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<property name="body"><![CDATA[h3. Normal Science meeting was usurped by discussion of progress on G3 development.

Doug led meeting with progress to date on design approach.
* Took a Systems Engineering approach, which focuses on the _functions_ we are looking for.

&nbsp;What do we currently know:
# Volume of G2 components
# G3 target and margins
# &nbsp;
# &nbsp;
# &nbsp;]]></property>
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<property name="body"><![CDATA[h3. Normal Science meeting was usurped by discussion of progress on G3 development.

Doug led meeting with progress to date on design approach.
* Took a Systems Engineering approach, which focuses on the _functions_ we are looking for.

&nbsp;What do we currently know:
# Volume of G2 components
# G3 target and margins

{gliffy:name=volume margins|space=ESPAPP|page=ESP -- SURF Center Main Page|pageid=2162822|align=left|size=M}

# &nbsp;
# &nbsp;
# &nbsp;]]></property>
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<property name="body"><![CDATA[h3. Normal Science meeting was usurped by discussion of progress on G3 development.

Doug led meeting with progress to date on design approach.
* Took a Systems Engineering approach, which focuses on the _functions_ we are looking for.

&nbsp;What do we currently know:
# Volume of G2 components
# G3 target and margins (considering a 2' extension to the LRAUV)

{gliffy:name=volume margins|space=ESPAPP|page=ESP -- SURF Center Main Page|pageid=2162822|align=left|size=M}
Right now, dry housing will hold 20 liters&nbsp; (current surface can is 200 liters)

3. G3 system design by function
\--this is Doug's "design dependencies" slide
4.&nbsp; Has 'cost' spreadsheet; helps predict leading costs--currently is Volume.&nbsp; This model was run on G2 and came up with 171L, close to can's 210L)
5.&nbsp; First run on G3 concept has run through the predictor. ]]></property>
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<property name="body"><![CDATA[h3. Normal Science meeting was usurped by discussion of progress on G3 development.

Doug led meeting with progress to date on design approach.
* Took a Systems Engineering approach, which focuses on the _functions_ we are looking for.

&nbsp;What do we currently know:
# Volume of G2 components
# G3 target and margins (considering a 2' extension to the LRAUV)

{gliffy:name=volume margins|space=ESPAPP|page=ESP -- SURF Center Main Page|pageid=2162822|align=left|size=M}
Right now, dry housing will hold 20 liters&nbsp; (current surface can is 200 liters)

3. G3 system design by function
\--this is Doug's "design dependencies" slide
4.&nbsp; Has 'cost' spreadsheet; helps predict leading costs--currently is Volume.&nbsp; This model was run on G2 and came up with 171L, close to can's 210L)
5.&nbsp; First run on G3 concept has run through the predictor. 
]]></property>
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<property name="body"><![CDATA[h3. Normal Science meeting was usurped by discussion of progress on G3 development.

Doug led meeting with progress to date on design approach.
* Took a Systems Engineering approach, which focuses on the _functions_ we are looking for.

&nbsp;What do we currently know:
# Volume of G2 components
# G3 target and margins (considering a 2' extension to the LRAUV)

{gliffy:name=volume margins|space=ESPAPP|page=ESP -- SURF Center Main Page|pageid=2162822|align=left|size=M}
Right now, dry housing will hold 20 liters&nbsp; (current surface can is 200 liters)

3. G3 system design by function
\--this is Doug's "design dependencies" slide
4.&nbsp; Has 'cost' spreadsheet; helps predict leading costs--currently is Volume.&nbsp; This model was run on G2 and came up with 171L, close to can's 210L)
5.&nbsp; First run on G3 concept has run through the predictor. 
{gliffy:name=LRAUV mechanical |space=ESPAPP|page=Mar 22|pageid=16416873|align=left|size=L}]]></property>
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<property name="body"><![CDATA[h3. Normal Science meeting was usurped by discussion of progress on G3 development.

Doug led meeting with progress to date on design approach.
* Took a Systems Engineering approach, which focuses on the _functions_ we are looking for.

h4. &nbsp;What do we currently know:

# Volume of G2 components
# G3 target and margins (considering a 2' extension to the LRAUV)

{gliffy:name=volume margins|space=ESPAPP|page=ESP -- SURF Center Main Page|pageid=2162822|align=left|size=M}
Right now, dry housing will hold 20 liters&nbsp; (current surface can is \~200 liters)

3. G3 system design by function
\--this is Doug's "design dependencies" slide
4.&nbsp; Has 'cost' spreadsheet; helps predict leading costs--currently is Volume.&nbsp; This model was run on G2 and came up with 171L, close to can's 210L)
5.&nbsp; First run on G3 concept has run through the predictor.

h4. Concepts developed

1.&nbsp; Fictional G3;&nbsp; this is the solidworks model everyone has
2.&nbsp; Pizza slice idea

h4. Refinement of Functional Requirements

Some things we still need to know:1.&nbsp; What contextual sensors will be on the AUV?&nbsp; CTD?&nbsp; ISUS?

2.&nbsp; LRAUV needs some 'payload' space in order to fly. (ADCP, compass).&nbsp; How does that cut into 'our' space?

h4. &nbsp;Designs we have chosen to bring forward

1.&nbsp; Linux/Ruby
2.&nbsp; new CPU (Brent has chosen)
3.&nbsp; Reuse Dwarf cards bu change CPLD to FPGA
4.&nbsp; Will use power from vehicle, but they have not provided a power budget.

5.&nbsp; Mechanical:&nbsp; Must validate the extension of the AUV&nbsp; (NOTE: contacted Jim Bellingham who suggested working with their hydrodynamic modeler.&nbsp; Awaiting contact \[3-22\]) ]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]

Once this model was developed to capture the concept that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. There are basically three "Groups" of functionality that are being worked on for the GUI.  The three areas are:

# Mission Planning
# Data Management and Access
# Instrument State Monitoring (and control at future date ... like way out there)

As a first cut at a GUI, a mockup was created and we just put tabs in to differentiate between the different groups of functionality.  The view shown here is from the mission planning perspective.  You can see that even though the components are differentiated, they have spilled over into each other.  In other words from the planning GUI, you can see data.

{mockup:Top Level|2}
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]

Once this model was developed to capture the concept that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. There are basically three "Groups" of functionality that are being worked on for the GUI.  The three areas are:

# Mission Planning
# Data Management and Access
# Instrument State Monitoring (and control at future date ... like way out there)

{mockup:Top Level|2}
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):

# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

As a first cut at a GUI, a mockup was created and we just put tabs in to differentiate between the different groups of functionality.  The view shown here is from the mission planning perspective.  You can see that even though the components are differentiated, they have spilled over into each other.  In other words from the planning GUI, you can see data.

{mockup:Top Level|2}
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):

# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:

# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).
# Then I decide I want to examine one particular instrument.  I select which instrument I am interested in and then can get more details on the deployments (past, current, and planned) by selecting the various deployments.


As a first cut at a GUI, a mockup was created and we just put tabs in to differentiate between the different groups of functionality.  The view shown here is from the mission planning perspective.  You can see that even though the components are differentiated, they have spilled over into each other.  In other words from the planning GUI, you can see data.

{mockup:Top Level|2}
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):

# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType (these are constructed from ProtocolTypes)
# Edit PhaseType
# Delete PhaseType
# Create Consumable
# Edit Consumable
# Delete Consumable

As a first cut at a GUI, a mockup was created and we just put tabs in to differentiate between the different groups of functionality.  The view shown here is from the mission planning perspective.  You can see that even though the components are differentiated, they have spilled over into each other.  In other words from the planning GUI, you can see data.

{mockup:Top Level|2}
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically There are basically three "Groups" of functionality that are being worked on for the GUI.  The three areas are:

# Mission Planning
# Data Management and Access
# Instrument State Monitoring (and control at future date ... like way out there)

As a first cut at a GUI, a mockup was created and we just put tabs in to differentiate between the different groups of functionality.  The view shown here is from the mission planning perspective.  You can see that even though the components are differentiated, they have spilled over into each other.  In other words from the planning GUI, you can see data.

{mockup:Top Level|2}
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# Feb 24 -- ad hoc
# Mar 3 -- CMORE Hawaii
# [Mar 10]]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):

# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:

# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).
# Then I decide I want to examine one particular instrument.  I select which instrument I am interested in and then can get more details on the deployments (past, current, and planned) by selecting the various deployments.

As a first cut at a GUI, a mockup was created and we just put tabs in to differentiate between the different groups of functionality.  The view shown here is from the mission planning perspective.  You can see that even though the components are differentiated, they have spilled over into each other.  In other words from the planning GUI, you can see data.

{mockup:Top Level|4}
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):

# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:

# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).
# Then I decide I want to examine one particular instrument.  I select which instrument I am interested in and then can get more details on the deployments (past, current, and planned) by selecting the various deployments.

As a first cut at a GUI, a mockup was created and we just put tabs in to differentiate between the different groups of functionality.  The view shown here is from the mission planning perspective.  You can see that even though the components are differentiated, they have spilled over into each other.  In other words from the planning GUI, you can see data.

{mockup:Top Level|3}
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}MAKAI flight w 4 Archives, 1 Lyse-n-go{color}

*Feb 2-4, 2016*

Repeat of Dec flight.&nbsp; Here are notes from Yanwu's summary:

(Note: when reaching each target depth (peak-chl or pre-set), we give Makai 10 minutes to damp down depth undulation.)

Sample#1 (lyse&go sample. At chl peak):
Makai descended from surface, found the chl peak at 8.7m. On the ensuing ascent, Makai held depth at 8.7m, and triggered sample#1.
Took 63 minutes to complete.&nbsp; Then Makai surfaced to "report to shore".

Sample#2 (archive sample. At chl peak):
Makai descended from surface, found the chl peak at 12.7m. On the ensuing ascent, Makai held depth at 12.3m, and triggered sample#2. (Note: the water column was quite mixed vertically. The chl values at 8m and 12m were very close. Makai was doing her best to pick the relatively weak peak.)&nbsp; Took 41 minutes to complete.

Sample#3 (archive sample. At reacquired chl peak):
In order to reacquire the chl peak (considering the peak-chl layer may have moved up or down), Makai intentionally wiggled up and down (up first, then down, and then up). On the "down", it found the chl peak at 13.2m. On the ensuing "up", Makai held depth at 13.0m, and triggered sample#3.&nbsp; Took 40 minutes to complete.

Sample#4 (archive sample. At pre-set 27m. Control sample.):
Makai dove to the pre-set 27m depth, and triggered sample#4.&nbsp; Took 39 minutes to complete.

Sample#5 (archive sample. At pre-set 27m. Control sample.):
Makai stayed at the pre-set 27m depth, and triggered sample#5.&nbsp; Took 38 minutes to complete.

h4. {color:#ff00cc}Del Mar--ESP-Waldo{color}

*May 17, 2016*

Used M/V Merlin (Walt Crampton), with MBARI surface mooring.&nbsp; Divers from SCRIPPS.&nbsp; Deployed with CTD about 400 yds from Del Mar mooring (SE of their mooring). Used new anchor line, #1 shockle, and 35m EM cable.

Ship coordinates when we dropped it:&nbsp; 32' 55.603N&nbsp; 117' 18.895W
Melo coordinates (IMEI: 300034012090780):&nbsp; 32.92633 \-117.31491

Water depth 100m.&nbsp; Divers reported master link at 22.8m, can top at 16.76m.&nbsp; CTD reading \~18m.

Initial mission is to take a sample two hours after sunrise, every weekday.
\\

h4.


h4. {color:#ff00cc}ESP-Moe;&nbsp; Moran in Monterey Bay{color}

*Sep 26, 2016*

After two-day wait for weather to settle, deployed ESP MOE at M0.&nbsp; No  mission loaded, as they wanted to manually fire each archive and have  more control over when they would manually collect samples.

Shana Rae used, with Charles Bock & Mike Conway diving.&nbsp; 15.6m EM cable with Shockle #2.&nbsp; CTD is around 5.65m deep.

Oct 7, lost comms to Moe.&nbsp; Modem and Cell provider check out.&nbsp;  Electrical signal up/down EM cable check out.&nbsp; Oct 11 bring out computer  to see if we can talk to can.

&nbsp;*Oct 13, 2016*

&nbsp;Got Shana Rae and divers (Eric + George) at the last minute.&nbsp; Weather beautiful. Flat.&nbsp; Recovered instrument on deck, and tried three ways to tunnel in to talk to host.&nbsp; No luck.&nbsp; Brought instrument home and could not communicate with host after uncanning.&nbsp; Scott traded carrier board with one in Brent's office and it worked.&nbsp; Moe carrier board did not work on another Sleepy.&nbsp; Work continues to discover why/ what went wrong on carrier board.

&nbsp;*Oct 27, 2016*

&nbsp;Got Shana Rae and divers (Jeff S and Paul C.).&nbsp;  Deployment went very smoothly.&nbsp; difficult cell phone reception at site.&nbsp; Got confirmation of depth (6.7m) and started home.&nbsp; After about 15 minutes got call from Brent that carousel was jammed and would not turn.&nbsp; Suggested recover.&nbsp; We returned and recovered and brought everything home.&nbsp; inspection showed that a carousel rod had unscrewed itself,fallen, and jammed against the elevator, freezing the carousel.&nbsp; Weather is turning more mercurial; will try to redeploy on Wed, Nov 2.
\\

*Nov 2, 2016* &nbsp;

Got Shana Rae and divers (Jeff S and Mike C).&nbsp; Deployment went smoothly, although had to wait for fueling of WF on dock.&nbsp; Left 11:30am, returned \~3pm.&nbsp; Depth 6.5m.&nbsp; This will be a 2-week run.]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):

# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:

# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).
# Then I decide I want to examine one particular instrument.  I select which instrument I am interested in and then can get more details on the deployments (past, current, and planned) by selecting the various deployments.


As a first cut at a GUI, a mockup was created and we just put tabs in to differentiate between the different groups of functionality.  The view shown here is from the mission planning perspective.  You can see that even though the components are differentiated, they have spilled over into each other.  In other words from the planning GUI, you can see data.

{mockup:Top Level|3}
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [E/M cables]
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Bill, Elif, Brent, Chris P, Doug, Scott, John, Roman

Absent: Chris S.\\

h3.


h3. JdF Preparations
\\

1.&nbsp; Doug sent out the following schematic for the wand design:
\\ !JdeF Wand.png|thumbnail!
* Pete had some questions about wand height and how adjustable it might be in a rocky, uneven environment.&nbsp; We will get the pilots involved in these discussions.
* ISMS--Charles still working on it.&nbsp; They will send to us by the {color:#ff0000}end of April{color}, if not sooner.
* Berthing:&nbsp; Who is going on the cruise is still TBD.&nbsp; Harvard would like 3 berths (2 male, 1 female)--if there is room Dan Rogers might like to go.&nbsp; There was also suggestion to bring Karen Loyd for the ride (if room).&nbsp; Bill U. is working on this list and we will discuss at next week's science meeting.
* do we want Pete's mass spec temperature logger?&nbsp; Yes.&nbsp; He will ship. \\

h3. &nbsp;Adaptive Sampling

&nbsp;Brent has created a simulation and provided a great demo of the code that triggers on certain contextual thresholds.&nbsp; He rec'd some input from Science on some tweaks.&nbsp; Yanwu returns next week, and he and Brent will work together to put Yanwu's code into Ruby.

h3. M0 Spring Deployment

* Chris and Roman making excellent progress
** MOE will have reagents by end of today
** MFB gets mated on Monday
** QC tests next week
** Week of March 21 we'll test adaptive sampling
** Can on April 1
** Deploy April 7

* There was some discussion of the Zephyr also deploying another instrument at M0, using our cruise.&nbsp; Will check on this.

h3. &nbsp;WHOI Deployment

&nbsp;All systems moving forward.&nbsp; Turner Calvis (?) is the guy to contact at UCONN regarding divers.&nbsp; Roman is on this.

We have selected site #3 as our deployment site.&nbsp; Notice to Mariner info has been given to Mike Kelly.&nbsp; He is waiting for contact person from WHOI in order to submit.
\\ !ESP locations_2011v14_3_9v2.png|thumbnail!

h3. D-ESP

DWSM has been reassembled but not torqued closed for high-pressure testing.&nbsp; We've ordered our own set of tools for that.&nbsp; Also found that the empty switch in the sample can does not work.&nbsp; This will need replacing, but high-pressure testing can continue before tearing everything open again.&nbsp; Must be careful not to squeeze the bag empty.

h3. &nbsp;Drifter

Will have a meeting of Brent, Scott, and Gene on Monday, 2pm.
\\]]></property>
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<property name="body"><![CDATA[h3. Meeting Notes
# [PDR Notes|Project Memos Minutes]
# [Meeting with Chris, June 11, 2007]
# [ESP GUI Demo and Questions|2007_09_05]
# [Follow up meeting on Resources and Consumables|2008_01_08]
# [Mock Mission Planning Meeting|2008_03_11]

h3. Requirements
# [Requirements]

h3. Supporting Documents
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]

h3. To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]

h3. Project Documentation:
# [Requirements (and Gathering)|Requirements (and Gathering) Documentation]
# [Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]

]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]

h3. Project Documentation:
# [Requirements Gathering|Requirements Gathering Documentation]
# [Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]

]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]

h3. To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]

h3. Project Documentation:
# [Requirements Gathering|Requirements Gathering Documentation]
# [Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]

]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]

{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]

h3. To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]

h3. Project Documentation:
# [Requirements (and Gathering)|Requirements Gathering Documentation]
# [Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]

]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

Diagram of existing logical deployment structure

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of 

After creating this view of the current layout, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]
]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

Diagram of existing logical deployment structure

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The naming convention goes:
## YYMMM
### espname
#### esp
So that means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.

After creating this view of the current layout, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]
]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

Diagram of existing logical deployment structure

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on \\tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp

After creating this view of the current layout, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]
]]></property>
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<property name="body"><![CDATA[Documentation for the Design of the GUI Application for the ESP Instrument

# [Data Model]
]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

Diagram of existing logical deployment structure

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, that might 

After creating this view of the current layout, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]
]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

[^Logical Deployment Diagram.jpg]

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on \\tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp

After creating this view of the current layout, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]
]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp

After creating this view of the current layout, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

[^Logical Deployment Diagram.jpg]

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on \\tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp

After creating this view of the current layout, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]
]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

[^Logical Deployment Diagram.jpg|thumbnail!]

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on \\tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp

After creating this view of the current layout, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.

# [Data Model]
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[
As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

{mockup:Top Level|1}
]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]
Once this model was developed to capture the concept that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. There are basically three "Groups" of functionality that are being worked on for the GUI.  The three areas are:
# Mission Planning
# Data Management and Access
# Instrument State Monitoring (and control at future date ... like way out there)

{mockup:Top Level|2}
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<property name="body"><![CDATA[
As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

{mockup:Top Level|2}
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<property name="body"><![CDATA[# [SHA development protocol] (v.1--Dec 20, 2012)]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

After creating this view of the current layout, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
{panel}

{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
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<property name="body"><![CDATA[{mockup:Top Level|1}

As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!

Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.4|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.4%2004_05_2008.doc]
# [PCR Users Manual v1.0|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20PCR%20Module%20Users%20Manual%20V1.0.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram4-09-08.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.3|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.3%2028_12_2007.doc]
# [PCR Users Manual v1.0|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20PCR%20Module%20Users%20Manual%20V1.0.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram4-09-08.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]
# [04Sep2008]]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}MAKAI flight w 4 Archives, 1 Lyse-n-go{color}

*Feb 2-4, 2016*

Repeat of Dec flight.&nbsp; Here are notes from Yanwu's summary:

(Note: when reaching each target depth (peak-chl or pre-set), we give Makai 10 minutes to damp down depth undulation.)

Sample#1 (lyse&go sample. At chl peak):
Makai descended from surface, found the chl peak at 8.7m. On the ensuing ascent, Makai held depth at 8.7m, and triggered sample#1.
Took 63 minutes to complete.&nbsp; Then Makai surfaced to "report to shore".

Sample#2 (archive sample. At chl peak):
Makai descended from surface, found the chl peak at 12.7m. On the ensuing ascent, Makai held depth at 12.3m, and triggered sample#2. (Note: the water column was quite mixed vertically. The chl values at 8m and 12m were very close. Makai was doing her best to pick the relatively weak peak.)&nbsp; Took 41 minutes to complete.

Sample#3 (archive sample. At reacquired chl peak):
In order to reacquire the chl peak (considering the peak-chl layer may have moved up or down), Makai intentionally wiggled up and down (up first, then down, and then up). On the "down", it found the chl peak at 13.2m. On the ensuing "up", Makai held depth at 13.0m, and triggered sample#3.&nbsp; Took 40 minutes to complete.

Sample#4 (archive sample. At pre-set 27m. Control sample.):
Makai dove to the pre-set 27m depth, and triggered sample#4.&nbsp; Took 39 minutes to complete.

Sample#5 (archive sample. At pre-set 27m. Control sample.):
Makai stayed at the pre-set 27m depth, and triggered sample#5.&nbsp; Took 38 minutes to complete.

h4. {color:#ff00cc}Del Mar--ESP-Waldo{color}

*May 17, 2016*

Used M/V Merlin (Walt Crampton), with MBARI surface mooring.&nbsp; Divers from SCRIPPS.&nbsp; Deployed with CTD about 400 yds from Del Mar mooring (SE of their mooring). Used new anchor line, #1 shockle, and 35m EM cable.

Ship coordinates when we dropped it:&nbsp; 32' 55.603N&nbsp; 117' 18.895W
Melo coordinates (IMEI: 300034012090780):&nbsp; 32.92633 \-117.31491

Water depth 100m.&nbsp; Divers reported master link at 22.8m, can top at 16.76m.&nbsp; CTD reading \~18m.

Initial mission is to take a sample two hours after sunrise, every weekday.
\\

h4.


h4. {color:#ff00cc}ESP-Moe;&nbsp; Moran in Monterey Bay{color}

*Sep 26, 2016*

After two-day wait for weather to settle, deployed ESP MOE at M0.&nbsp; No  mission loaded, as they wanted to manually fire each archive and have  more control over when they would manually collect samples.

Shana Rae used, with Charles Bock & Mike Conway diving.&nbsp; 15.6m EM cable with Shockle #2.&nbsp; CTD is around 5.65m deep.

Oct 7, lost comms to Moe.&nbsp; Modem and Cell provider check out.&nbsp;  Electrical signal up/down EM cable check out.&nbsp; Oct 11 bring out computer  to see if we can talk to can.

&nbsp;*Oct 13, 2016*

&nbsp;Got Shana Rae and divers (Eric + George) at the last minute.&nbsp; Weather beautiful. Flat.&nbsp; Recovered instrument on deck, and tried three ways to tunnel in to talk to host.&nbsp; No luck.&nbsp; Brought instrument home and could not communicate with host after uncanning.&nbsp; Scott traded carrier board with one in Brent's office and it worked.&nbsp; Moe carrier board did not work on another Sleepy.&nbsp; Work continues to discover why/ what went wrong on carrier board.

&nbsp;*Oct 27, 2016*

&nbsp;Got Shana Rae and divers (Jeff S and Paul C.).&nbsp;  Deployment went very smoothly.&nbsp; difficult cell phone reception at site.&nbsp; Got confirmation of depth (6.7m) and started home.&nbsp; After about 15 minutes got call from Brent that carousel was jammed and would not turn.&nbsp; Suggested recover.&nbsp; We returned and recovered and brought everything home.&nbsp; inspection showed that a carousel rod had unscrewed itself,fallen, and jammed against the elevator, freezing the carousel.&nbsp; Weather is turning more mercurial; will try to redeploy on Wed, Nov 2.
\\]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}MAKAI flight w 4 Archives, 1 Lyse-n-go{color}

*Feb 2-4, 2016*

Repeat of Dec flight.&nbsp; Here are notes from Yanwu's summary:

(Note: when reaching each target depth (peak-chl or pre-set), we give Makai 10 minutes to damp down depth undulation.)

Sample#1 (lyse&go sample. At chl peak):
Makai descended from surface, found the chl peak at 8.7m. On the ensuing ascent, Makai held depth at 8.7m, and triggered sample#1.
Took 63 minutes to complete.&nbsp; Then Makai surfaced to "report to shore".

Sample#2 (archive sample. At chl peak):
Makai descended from surface, found the chl peak at 12.7m. On the ensuing ascent, Makai held depth at 12.3m, and triggered sample#2. (Note: the water column was quite mixed vertically. The chl values at 8m and 12m were very close. Makai was doing her best to pick the relatively weak peak.)&nbsp; Took 41 minutes to complete.

Sample#3 (archive sample. At reacquired chl peak):
In order to reacquire the chl peak (considering the peak-chl layer may have moved up or down), Makai intentionally wiggled up and down (up first, then down, and then up). On the "down", it found the chl peak at 13.2m. On the ensuing "up", Makai held depth at 13.0m, and triggered sample#3.&nbsp; Took 40 minutes to complete.

Sample#4 (archive sample. At pre-set 27m. Control sample.):
Makai dove to the pre-set 27m depth, and triggered sample#4.&nbsp; Took 39 minutes to complete.

Sample#5 (archive sample. At pre-set 27m. Control sample.):
Makai stayed at the pre-set 27m depth, and triggered sample#5.&nbsp; Took 38 minutes to complete.

h4. {color:#ff00cc}Del Mar--ESP-Waldo{color}

*May 17, 2016*

Used M/V Merlin (Walt Crampton), with MBARI surface mooring.&nbsp; Divers from SCRIPPS.&nbsp; Deployed with CTD about 400 yds from Del Mar mooring (SE of their mooring). Used new anchor line, #1 shockle, and 35m EM cable.

Ship coordinates when we dropped it:&nbsp; 32' 55.603N&nbsp; 117' 18.895W
Melo coordinates (IMEI: 300034012090780):&nbsp; 32.92633 \-117.31491

Water depth 100m.&nbsp; Divers reported master link at 22.8m, can top at 16.76m.&nbsp; CTD reading \~18m.

Initial mission is to take a sample two hours after sunrise, every weekday.
\\

h4.


h4. {color:#ff00cc}ESP-Moe;&nbsp; Moran in Monterey Bay{color}

*Sep 26, 2016*

After two-day wait for weather to settle, deployed ESP MOE at M0.&nbsp; No  mission loaded, as they wanted to manually fire each archive and have  more control over when they would manually collect samples.

Shana Rae used, with Charles Bock & Mike Conway diving.&nbsp; 15.6m EM cable with Shockle #2.&nbsp; CTD is around 5.65m deep.

Oct 7, lost comms to Moe.&nbsp; Modem and Cell provider check out.&nbsp;  Electrical signal up/down EM cable check out.&nbsp; Oct 11 bring out computer  to see if we can talk to can.

&nbsp;*Oct 13, 2016*

&nbsp;Got Shana Rae and divers (Eric + George) at the last minute.&nbsp; Weather beautiful. Flat.&nbsp; Recovered instrument on deck, and tried three ways to tunnel in to talk to host.&nbsp; No luck.&nbsp; Brought instrument home and could not communicate with host after uncanning.&nbsp; Scott traded carrier board with one in Brent's office and it worked.&nbsp; Moe carrier board did not work on another Sleepy.&nbsp; Work continues to discover why/ what went wrong on carrier board.]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}MAKAI flight w 4 Archives, 1 Lyse-n-go{color}

*Feb 2-4, 2016*

Repeat of Dec flight.&nbsp; Here are notes from Yanwu's summary:

(Note: when reaching each target depth (peak-chl or pre-set), we give Makai 10 minutes to damp down depth undulation.)

Sample#1 (lyse&go sample. At chl peak):
Makai descended from surface, found the chl peak at 8.7m. On the ensuing ascent, Makai held depth at 8.7m, and triggered sample#1.
Took 63 minutes to complete.&nbsp; Then Makai surfaced to "report to shore".

Sample#2 (archive sample. At chl peak):
Makai descended from surface, found the chl peak at 12.7m. On the ensuing ascent, Makai held depth at 12.3m, and triggered sample#2. (Note: the water column was quite mixed vertically. The chl values at 8m and 12m were very close. Makai was doing her best to pick the relatively weak peak.)&nbsp; Took 41 minutes to complete.

Sample#3 (archive sample. At reacquired chl peak):
In order to reacquire the chl peak (considering the peak-chl layer may have moved up or down), Makai intentionally wiggled up and down (up first, then down, and then up). On the "down", it found the chl peak at 13.2m. On the ensuing "up", Makai held depth at 13.0m, and triggered sample#3.&nbsp; Took 40 minutes to complete.

Sample#4 (archive sample. At pre-set 27m. Control sample.):
Makai dove to the pre-set 27m depth, and triggered sample#4.&nbsp; Took 39 minutes to complete.

Sample#5 (archive sample. At pre-set 27m. Control sample.):
Makai stayed at the pre-set 27m depth, and triggered sample#5.&nbsp; Took 38 minutes to complete.

h4. {color:#ff00cc}Del Mar--ESP-Waldo{color}

*May 17, 2016*

Used M/V Merlin (Walt Crampton), with MBARI surface mooring.&nbsp; Divers from SCRIPPS.&nbsp; Deployed with CTD about 400 yds from Del Mar mooring (SE of their mooring). Used new anchor line, #1 shockle, and 35m EM cable.

Ship coordinates when we dropped it:&nbsp; 32' 55.603N&nbsp; 117' 18.895W
Melo coordinates (IMEI: 300034012090780):&nbsp; 32.92633 \-117.31491

Water depth 100m.&nbsp; Divers reported master link at 22.8m, can top at 16.76m.&nbsp; CTD reading \~18m.

Initial mission is to take a sample two hours after sunrise, every weekday.
\\

h4.


h4. {color:#ff00cc}ESP-Moe;&nbsp; Moran in Monterey Bay{color}

*Sep 26, 2016*

After two-day wait for weather to settle, deployed ESP MOE at M0.&nbsp; No  mission loaded, as they wanted to manually fire each archive and have  more control over when they would manually collect samples.

Shana Rae used, with Charles Bock & Mike Conway diving.&nbsp; 15.6m EM cable with Shockle #2.&nbsp; CTD is around 5.65m deep.


Oct 7, lost comms to Moe.&nbsp; Modem and Cell provider check out.&nbsp;  Electrical signal up/down EM cable check out.&nbsp; Oct 11 bring out computer  to see if we can talk to can.]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}MAKAI flight w 4 Archives, 1 Lyse-n-go{color}

*Feb 2-4, 2016*

Repeat of Dec flight.&nbsp; Here are notes from Yanwu's summary:

(Note: when reaching each target depth (peak-chl or pre-set), we give Makai 10 minutes to damp down depth undulation.)

Sample#1 (lyse&go sample. At chl peak):
Makai descended from surface, found the chl peak at 8.7m. On the ensuing ascent, Makai held depth at 8.7m, and triggered sample#1.
Took 63 minutes to complete.&nbsp; Then Makai surfaced to "report to shore".

Sample#2 (archive sample. At chl peak):
Makai descended from surface, found the chl peak at 12.7m. On the ensuing ascent, Makai held depth at 12.3m, and triggered sample#2. (Note: the water column was quite mixed vertically. The chl values at 8m and 12m were very close. Makai was doing her best to pick the relatively weak peak.)&nbsp; Took 41 minutes to complete.

Sample#3 (archive sample. At reacquired chl peak):
In order to reacquire the chl peak (considering the peak-chl layer may have moved up or down), Makai intentionally wiggled up and down (up first, then down, and then up). On the "down", it found the chl peak at 13.2m. On the ensuing "up", Makai held depth at 13.0m, and triggered sample#3.&nbsp; Took 40 minutes to complete.

Sample#4 (archive sample. At pre-set 27m. Control sample.):
Makai dove to the pre-set 27m depth, and triggered sample#4.&nbsp; Took 39 minutes to complete.

Sample#5 (archive sample. At pre-set 27m. Control sample.):
Makai stayed at the pre-set 27m depth, and triggered sample#5.&nbsp; Took 38 minutes to complete.

h4. {color:#ff00cc}Del Mar--ESP-Waldo{color}

*May 17, 2016*

Used M/V Merlin (Walt Crampton), with MBARI surface mooring.&nbsp; Divers from SCRIPPS.&nbsp; Deployed with CTD about 400 yds from Del Mar mooring (SE of their mooring). Used new anchor line, #1 shockle, and 35m EM cable.

Ship coordinates when we dropped it:&nbsp; 32' 55.603N&nbsp; 117' 18.895W
Melo coordinates (IMEI: 300034012090780):&nbsp; 32.92633 \-117.31491

Water depth 100m.&nbsp; Divers reported master link at 22.8m, can top at 16.76m.&nbsp; CTD reading \~18m.

Initial mission is to take a sample two hours after sunrise, every weekday. \\

h4. {color:#ff00cc}Moran Deployment M0--ESP-Moe{color}

*Sep 22, 2016*

Used Shana Rae.
\\]]></property>
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<property name="body"><![CDATA[h2. Overview

h2. Notes

The printer used by [~scholin] is a custom printer. It can not output GAL files. It does put out a text file that I'm trying to parse and work with. A copy of the file is checked into [SVN|http://kahuna.shore.mbari.org/viewvc.cgi/esp/trunk/esp-imaging/src/test/resources/imaging/2_22_08comptest_2008-02-25_142348_Run.txt?view=markup].

h3. Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:
{noformat}
SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK
{noformat}

_SpotX_ and _SpotY_ are coordinates in micrometers starting in the upper left hand corner of the paper. The _0, 0_ point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out.

_SrcWell_ indicates the contents of the spots. For example, all spots from the _C-1_ source well will have identical chemistries applied.

h3. Image Analysis

Maximum Entropy thresholding does a decent job of delineating the control spots. Unfortunately, I haven't found a technique for delineating the spots that don't go off. In fact those spots can contain values within the range of the background noise. 

{gallery}

h4. Possible avenues of exploration

The ESP folks would like an automated image analysis package that:
# Reads the image
# locates the spots (either with or without the help of the GAL-like file)
# Read the highest 8x8 block (full size image) or 4x4 block (half-size image) average within the spot. The block average is square with no weighting applied.
# Return a text file (Tab or comma delimited) with:
#* Average intensity associated with the _SrcWell_ (i.e. C-1, A-1, etc.)
#* Standard deviation by _SrcWell_
#* Average intensity of background disk (excluding spot values)

h4. Road map
# Read GAL-like file and list of _SrcWell_ ID's representing control spots
# Generate control image


h3. References
# Old ESP Matlab toolbox at [http://moonjelly/cgi-bin/cvsweb.cgi/ESP/matlab/]
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]
# [04Sep2008]
# [11Sep2008]
# [18Sep2008]]]></property>
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<property name="body"><![CDATA[{mockup:Data_Import|1}

As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[h3. Deployment Update

* October deployment:
h6. {color:#ff0099}Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs){color}

* {color:#000000}Mission is defined for NEO.&nbsp; Still to do for Mack and Bruce but should be straightforward{color}
* {color:#000000}Small Array format being difficult.&nbsp; Will make call by end of day today on whether we can make it work;&nbsp; we're very close, but may punt on it.{color}
* {color:#000000}If it works, need Brent to work on software integration.&nbsp; He may work on it over weekend.{color}

h3. Machine Builds

* Moe--elbow still not working.&nbsp; Scott conferring with engineers within company.&nbsp; Mike working on putting counter-bore into holder piece which may help alignment.
* Moe should be ready by Oct 13 visitors.
* Bumper for NEO ready
* Board checkout--Dick got host board.&nbsp; We need some dwarfs so Cheri/Addie may quickly check 2 out.&nbsp; Cheri will show Wayne how checkout works, tomorrow.

h3. MFB

* Much discussion of stand-pipe issue.&nbsp; Decision was to not change what works, since it hasn't loosened since people have stopped messin' with it.
* Brent fixed a problem with the serial cable from the PCR module to the dwarf; power cycling is no longer a problem
* Have had 2 time-out errors with the AS; it loses its position but dwarf is not reset.&nbsp; Brent will try upgrading firmware from v.2.50a(64Hz) to v.2.59a(64Hz).&nbsp; If this doesn't work, we'll try a new dwarf.
* Bruce 'brain-freeze' may have been a network problem.&nbsp; Brent changed from CAT 3 to CAT 5 cable in the B-lab.&nbsp; Still watching for hangups.
* Addie contacting PCR-tubing company for a remake; in meantime we will NOT be asking LLNL for more tubing, as it appears the current tubing works.


h3. Software

* Would like to freeze Mack/Bruce code by tomorrow (Friday).&nbsp; Start radio tests next week.&nbsp; Must exercise all assays to check out.
* Many chunks to stitch together for SAF to work on NEO.&nbsp; Much discussion on how long that may take and how much cutting into our cold testing is acceptable.&nbsp; Chris working with roman and brent on this.
* should re-name 'home syringe' on MFB (Addie).&nbsp; Discussion finalized a solution.
* Brent discovered they don't make the old CTD's anymore and there is question as to whether our drivers will work with the new CTD model.&nbsp; Decision is to use old CTD's on Mack and Bruce.&nbsp; We then can 1) borrow another older model, 2) use the deep CTD (with wacky pressure guage), or 3) get a new one and hope drivers work.
* Brent working on firmware today and will hand-off HEX files to Wayne

h3. DWSM

* Drawings for both plates finished and gone over with Ray
* Estimate is that Ray will be working on these until October 23
* Oatmeal can is now called the Thermos, and is finished
* Bell housings are here and check-out.
* Burn-rates on ASTEP and NSF are acceptable; if we need more shop labor time, Chris S. can charge less to grant.

h3. GUI Development

* Kevin out sick today, but stated the following in an email:


h3. Other Items:

* _Oceanography_ paper came in 6 pages over length limit, so we are not including photo of MFB mounted to core.&nbsp; Photoshoot next week is cancelled.]]></property>
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<property name="body"><![CDATA[h3. Deployment Update

* October deployment:
h6. {color:#ff0099}Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs){color}

* {color:#000000}Mission is defined for NEO.&nbsp; Still to do for Mack and Bruce but should be straightforward{color}
* {color:#000000}Small Array format being difficult.&nbsp; Will make call by end of day today on whether we can make it work;&nbsp; we're very close, but may punt on it.{color}
* {color:#000000}If it works, need Brent to work on software integration.&nbsp; He may work on it over weekend.{color}

h3. Machine Builds

* Moe--elbow still not working.&nbsp; Scott conferring with engineers within company.&nbsp; Mike working on putting counter-bore into holder piece which may help alignment.
* Moe should be ready by Oct 13 visitors.
* Bumper for NEO ready
* Board checkout--Dick got host board.&nbsp; We need some dwarfs so Cheri/Addie may quickly check 2 out.&nbsp; Cheri will show Wayne how checkout works, tomorrow.

h3. MFB

* Much discussion of stand-pipe issue.&nbsp; Decision was to not change what works, since it hasn't loosened since people have stopped messin' with it.
* Brent fixed a problem with the serial cable from the PCR module to the dwarf; power cycling is no longer a problem
* Have had 2 time-out errors with the AS; it loses its position but dwarf is not reset.&nbsp; Brent will try upgrading firmware from v.2.50a(64Hz) to v.2.59a(64Hz).&nbsp; If this doesn't work, we'll try a new dwarf.
* Bruce 'brain-freeze' may have been a network problem.&nbsp; Brent changed from CAT 3 to CAT 5 cable in the B-lab.&nbsp; Still watching for hangups.
* Addie contacting PCR-tubing company for a remake; in meantime we will NOT be asking LLNL for more tubing, as it appears the current tubing works.

h3. Software

* Would like to freeze Mack/Bruce code by tomorrow (Friday).&nbsp; Start radio tests next week.&nbsp; Must exercise all assays to check out.
* Many chunks to stitch together for SAF to work on NEO.&nbsp; Much discussion on how long that may take and how much cutting into our cold testing is acceptable.&nbsp; Chris working with roman and brent on this.
* should re-name 'home syringe' on MFB (Addie).&nbsp; Discussion finalized a solution.
* Brent discovered they don't make the old CTD's anymore and there is question as to whether our drivers will work with the new CTD model.&nbsp; Decision is to use old CTD's on Mack and Bruce.&nbsp; We then can 1) borrow another older model, 2) use the deep CTD (with wacky pressure gauge), or 3) get a new one and hope drivers work.
* Brent working on firmware today and will hand-off HEX files to Wayne

h3. DWSM

* Drawings for both plates finished and gone over with Ray
* Estimate is that Ray will be working on these until October 23
* Oatmeal can is now called the Thermos, and is finished
* Bell housings are here and check-out.
* Burn-rates on ASTEP and NSF are acceptable; if we need more shop labor time, Chris S. can charge less to grant.
* there is one piece of pressure testing for DWSM that is $6K.&nbsp; Approval given to purchase.

h3. GUI Development

* Kevin out sick today, but stated the following in an email:Jim, the ESP GUI should be ready for the mission planning exercise tomorrow and I will work to finish it up today and roll it out to production tomorrow AM.&nbsp; I can then work with Chris P (or whomever) to do the mission plan.&nbsp; I have started on the data access part and am hoping to have something working over the next couple of weeks before the deployment ...

h3. Other Items:

* _Oceanography_ paper came in 6 pages over length limit, so we are not including photo of MFB mounted to core.&nbsp; Photo-shoot next week is canceled.
* Research on renting a storage van has begun.&nbsp; ]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]
# [04Sep2008]
# [11Sep2008]]]></property>
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<property name="body"><![CDATA[Draft ESP cheatsheet as of 3/21/07

This will likely need to be put into a Word document.
Feedback appreciated...

\-----------\-
Preparation for running high level protocols in the lab:

0) Insure that no one else has is running the esp
&nbsp;&nbsp; application on the ESPhost machine

1)&nbsp; ssh to the ESPhost machine as the appropriate user
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (most often this will be user esp or scholin)
$ ssh user@espHost

2)&nbsp; confirm the ESP is getting the right code base
&nbsp;&nbsp;&nbsp; check the Using ... line that appears right after the login
&nbsp;&nbsp;&nbsp; It should say
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Using esp@espbook, ESPhome=/home/esp/esp2 for user scholin
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; or
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Using esp2local, ESPhome=/home/esp/esp2 for user esp

&nbsp;&nbsp;&nbsp; The message:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; WARNING:&nbsp; ESPhome is undefined\!

&nbsp;&nbsp;&nbsp; indicates a transient network filesystem problem (NFS).
&nbsp;&nbsp;&nbsp; If the machine is in a safe state, simply logout, cycle its
&nbsp;&nbsp;&nbsp; power and try again after 30 seconds or so.&nbsp; Alternatively,
&nbsp;&nbsp;&nbsp; you can login as the root use and type:

\# service nfsmount start

&nbsp;&nbsp;&nbsp; After the nfsmounts all complete, logout of root and
&nbsp;&nbsp;&nbsp; try logging in as scholin
&nbsp;&nbsp;&nbsp; again.&nbsp; You should not see this problem when logging in
&nbsp;&nbsp;&nbsp; as user esp, as this user does not rely on NFS mounts.


3)&nbsp; start the esp application

$ esp

4)&nbsp; Insure that the ESP is homed and ready:

esp>&nbsp; ESP.ready\!

5)&nbsp; Visually verify that the FlushPuck is in its garage.

Now, after loading the appropriate puck(s),
you will be ready to run your protocols as follows:

\[Whole Cell Archive\]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; wcr sampleVolume, bubblePt, fixTime=60*60, fixes=3, fixVolume=2

Example:
esp>&nbsp;&nbsp;&nbsp; startTube 3&nbsp;&nbsp;&nbsp;&nbsp; #pull WCR puck from tube 3, discard into tube 2
esp>&nbsp;&nbsp;&nbsp; wcr&nbsp; 200, 24&nbsp;&nbsp;&nbsp; #sample 200ml, filter bubblePoint of 24psi
\#defaults to 3 (20 minute) fixes of 2ml each.


\[Short Sandwich Hybridization phase 2 for in lab testing\]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; shortSh2(signal=:sig1, hash={}, &wcrBlock)

Examples:
esp>&nbsp;&nbsp;&nbsp; startTube 2&nbsp;&nbsp;&nbsp;&nbsp; #pull pucks from tube 2, discard into tube 1
esp>&nbsp;&nbsp;&nbsp; shortSh2 :sig2, :assay=>:bac&nbsp; #run BAC assay using :sig2

esp>&nbsp;&nbsp;&nbsp; shortSh2(:sig1, :assay=>:hab) {wcr 50, 24}
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #hab assay followed by wcr


\[Harmful Algae Bloom\]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; HAB(sampleVolume=400, wcrVol=50, &cleanup)&nbsp;&nbsp; #with initialPurge
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; hab(sampleVolume=400, wcrVol=50, &cleanup)&nbsp;&nbsp; #w/o initialPurge

Examples:
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; startTube 7&nbsp;&nbsp;&nbsp;&nbsp; #pull 4 pucks from tube 7, discard into 6
esp>&nbsp;&nbsp;&nbsp; HAB&nbsp;&nbsp;&nbsp; #sample 400ml, wcr 50ml, standard killIntake cleanup
esp>&nbsp;&nbsp;&nbsp; HAB 1200, 100&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #1200ml sample, 100ml wcr
esp>&nbsp;&nbsp;&nbsp; hab(1000) {endPurge}&nbsp; #1000ml sample
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #skip intialPurge, do not purge or kill Intake


\[Larval\]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; LARV(sampleVolume=400, wcrVol=50, &cleanup)&nbsp;&nbsp; #with initialPurge
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; larv(sampleVolume=400, wcrVol=50, &cleanup)&nbsp;&nbsp; #skip initialPurge

Examples:
esp>&nbsp;&nbsp;&nbsp; startTube 7&nbsp;&nbsp;&nbsp;&nbsp; #pull 4 pucks from tube 7, discard into 6
esp>&nbsp;&nbsp;&nbsp; LARV&nbsp;&nbsp;&nbsp; #sample 400ml, wcr 50ml, standard killIntake cleanup
esp>&nbsp;&nbsp;&nbsp; LARV 1200, 400&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #1200ml sample, 400ml wcr
esp>&nbsp;&nbsp;&nbsp; larv(1000) {endPurge}&nbsp; #1000ml sample
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #skip intialPurge, do not purge or kill Intake


\[Bacterial\]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; BAC(sampleVolume=100, wcrVol=50, &cleanup)&nbsp;&nbsp; #with initialPurge
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; bac(sampleVolume=100, &cleanup)&nbsp;&nbsp; #without initialPurge

Examples:
esp>&nbsp;&nbsp;&nbsp; startTube 5&nbsp;&nbsp;&nbsp;&nbsp; #pull 4 pucks from tube 5, discard into 4
esp>&nbsp;&nbsp;&nbsp; BAC&nbsp;&nbsp;&nbsp; #sample 100ml, wcr 50ml, standard killIntake cleanup
esp>&nbsp;&nbsp;&nbsp; HAB 1700, 800&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #1700ml sample, 800ml wcr
esp>&nbsp;&nbsp;&nbsp; bac(1500, 500) {endPurge}&nbsp; #1500ml sample, 500ml wcr
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #skip intialPurge, do not purge or kill Intake


\[Demoic Acid\]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; DA(sampleVolume=750, &cleanup)&nbsp;&nbsp; #with initialPurge
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; da(sampleVolume=750, &cleanup)&nbsp;&nbsp; #without initialPurge

Examples:
esp>&nbsp;&nbsp;&nbsp; startTube 6&nbsp;&nbsp;&nbsp;&nbsp; #pull 3 pucks from tube 6, discard into 4
esp>&nbsp;&nbsp;&nbsp; DA&nbsp;&nbsp;&nbsp; #sample 100ml, NO WCR, standard killIntake cleanup
esp>&nbsp;&nbsp;&nbsp; DA 1200&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #1200ml sample, no wcr
esp>&nbsp;&nbsp;&nbsp; da(1250) {\|ports\| endPurge(*ports)}&nbsp; #1250ml sample, no wcr
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #skip intialPurge, do not purge or kill Intake


\[Harmful Algae Bloom plus Demoic Acid\]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; HABDA(sampleVolume=400,daVolume=750,&cleanup)&nbsp; #w/initialPurge
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; HABDA(sampleVolume=400,daVolume=750,&cleanup)&nbsp; #w/o initialPurge

Examples:
esp>&nbsp;&nbsp;&nbsp; startTube 4&nbsp;&nbsp;&nbsp;&nbsp; #pull 7 pucks from tube 4, discard into 3
esp>&nbsp;&nbsp;&nbsp; HABDA&nbsp;&nbsp;&nbsp; #sample 400ml, wcr 50ml, DA 750ml,&nbsp; standard cleanup
esp>&nbsp;&nbsp;&nbsp; HABDA 500, 300&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #sample 500ml, DA 300ml, standard cleanup
esp>&nbsp;&nbsp;&nbsp; habda(1200, 500) {\|ports\| endPurge(*ports)}
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #1200ml sample, 500ml DA, (50ml wcr)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #skip intialPurge, do not purge or kill Intake

==============
Image Capture

All the above protocols (except wcr) take additional (optional)
:key=>:value type parameters that can be used to alter the image
capture settings.&nbsp; By default, three images are taken.

Image #1:&nbsp; 10 seconds with 4x4 binning
Image #2:&nbsp; 30 seconds with 4x4 binning
Image #3:&nbsp; hi-resolution Auto exposure

The :image key can be used to override this for a
given protocol run as follows:

esp>&nbsp;&nbsp;&nbsp; HAB 500, 50, :image=>\[5, :hires, 40, :auto, :midres, 20\]

This takes the following images:

Image #1:&nbsp; 5 seconds with default (4x4) binning
Image #2: 40 seconds with no binning (hi-resolution)
Image #3: hi-resolution Auto exposure
Image #4: 20 seoncds with 2x2 binning

See the Exposures, ImageMode and PuckCamera declarations in
shallow/configure.rb for more details on setting default
binning, image output directory, etc.


==============
Gigi's puck handling comands have undergone quite a bit of revision
over that past couple months.
Here's an updated command reference:

\*Puck Handling commands\*
\[This is copied from a mail I originally sent the list on 1/18/07\]


CC.loadPuck&nbsp; label, fromTube=nil
PC.loadPuck&nbsp; label, fromTube=nil
\# load a puck from the specified carousel tube into
\# the respective clamp (CC or PC).&nbsp; Use the required
\# puck label help to track it.&nbsp; Typical labels are:
\#&nbsp; :sh1, :sh2, :lyfil, :WCR, etc.&nbsp; The labels will soon enable
\# the ESP to produce instructions for loading
\# the carousel prior to a mission.&nbsp; For now, they
\# just show up as helpful comments in the log.
\# If the fromTube is not specified, then the puck
\# is taken from the currently defined "startTube"
\# If that "startTube" is empty, it advances
\# "startTube" to the next tube automatically.
\# This lets puck sets span tubes if desired.


CC.unloadPuck&nbsp; toTube=Storage.dstTube
PC.unloadPuck&nbsp; toTube=Storage.dstTube
\# unload puck in specified clamp to specified carousel tube.
\# If toTube is not specified, the puck is stored
\# in the "destination tube".&nbsp; For now, the "destination tube"
\# is simply one less than the current startTube.
\# For this reason, is it not advisible to set startTube to 1.


startTube&nbsp; tubeNumber=nil
\# define the current start or sourceTube for loadPuck.
\# if tubeNumber is omitted, the current startTube
\# is returned, unchanged.


dstTube
\# returns the current default destination tube for
\# unloadPuck.&nbsp; There is no way to set this explicitly.
\# For now, it is defined as 1 less than startTube.


access&nbsp; tubeNumber=SC.position.base
\# Rotate the carousel such that the specified tube
\# is accessible for manually loading and unloading pucks.
\# if tubeNumber is omitted, the currently selected
\# tube is made accessible.


CC.contains
PC.contains
\# return the label of the puck currently clamped
\# Handy if you've forgotten what's where...


Flush.to CC
Flush.to PC
CC.loadFlush
PC.loadFlush
\# all these simply load the flush puck into the specified clamp

Flush.garage clampledPos=nil
\# put the flush puck back into its garage
\# The clamp need not normally be specified, as the system
\# will track where the FlushPuck is currently clamped.
\# It may be specifed to explicity override the system's
\# record of the current FlushPucks position.


PC.unloadFlush
CC.unloadFlush
\# equivalent to
\#&nbsp; Flush.garage PC&nbsp; or&nbsp;&nbsp; Flush.garage&nbsp; CC


Puck.move&nbsp; fromTube, toTube
\# move the tube at the top of tube fromTube
\# to the top of top toTube


Puck.count&nbsp; tubes=1..SCtubes
\# count the number of pucks in the specified tubes
\# of tubes is omitted, count the # of pucks in all tubes.
\# This works by measuring the height of each respective
\# puck stack.


Storage.pucks
\# returns a hash of tube numbers to their respecive
\# puck stack heights.&nbsp; The unit of measure such that
\# 1.0 = one standard puck.&nbsp; The results are fractional
\# due to measurement errors and puck height variences.

Storage.pucks.sort.collect {\|x\| x.last ? x.last.round : x.last}
\# This incantation will return an array with each element
\# corresponding to the number of pucks in that tube.


=================

Multithreading has introduced the concept of locking the Arm and the
FlushPuck to a particular thread to ensure that no other thread can
hijack those resources while that are in use.&nbsp; The FlushPuck and Puck
load/unload commands handle this locking more or less transparently.
The Arm is locked for as long as it takes to complete the requested puck
move.&nbsp; The FlushPuck is locked whenever it is not garaged.

If a script attempts to move a puck while the Arm is locked, you will
see the message:

Waiting for (threadName) to free Arm
==or==
Waiting for (threadName) to free FlushPuck

Normally, the thread will eventually free the resource, allowing the waiting
thread to continue after claiming it.&nbsp; However,
The system can become confused if a puck movement is interrupted either
by an error or user abort.&nbsp; In this case, the thread that locked the Arm
and/or FlushPuck may be dead and the system in an indeterminate state.
The commands:

Arm.reset
FlushPuck.reset

May be used to in this case to reset the locks so that new threads may
access the resources.&nbsp; Normally, these command would be executed
only after the ESP was carefully inspected and returned to a safe state
using low level Arm.commands.&nbsp; For instance, if a user aborted loading
a FlushPuck into CC, the reovery sequence might be:

CC.open
Arm.releaseAt&nbsp; :garage
Arm.reset
FlushPuck.reset

Note that, if another thread is waiting on the resource, it will be able
to acquire it and continue after Arm/FlushPuck .reset.&nbsp; Therefore,
it is important not to reset until the system is put back into
a "safe" state.&nbsp; Also note that the primitive Arm.commands
do not respect the state of any locks, whereas the FlushPuck
and other higher-level puck movement commands do.
This rule allows users to interactively move the Arm to clear
errors without first resetting the locks.


And, a quicky new Arm command:

Arm.withdraw
\#retract the arm without opening the hand.]]></property>
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<property name="body"><![CDATA[h2.


h1. We currently (12-2012) have three Melo trackers

{color:#006600}The Melo is the 'watch-circle' warning transponder for surface moorings.{color}\\

IMEI numbers:

h3. *300034012090780&nbsp; (purchased June, 2011)*


h3. 300234060016190&nbsp; (serial # 122)&nbsp;&nbsp; (both purchased Dec, 2012)


h3. 300234060014550 (serial # 123)

\\

User's Manuals
# [Quick Start Guide v1.2|^Xeos_Melo_manual-1.pdf|quick start]
# [User Manual v1.5|^Melo_User_Manual _watch_circle_V1.5.pdf|Full Manual]
# [Watch Circle Console User Manual v2.1|^Xeos_Melo_manual-3.pdf|watch circle]\\]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|3}

{mockup:Protocol_Type_Dialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



]]></property>
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<property name="body"><![CDATA[{mockup:Protocol_Type_Dialog|1}

As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|2}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|2}

{mockup:Protocol_Type_Dialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[h2.


h1. We currently (12-2012) have three Melo trackers

{color:#006600}The Melo is the 'watch-circle' warning transponder for surface moorings.{color}\\

IMEI numbers:

h3. *300034012090780&nbsp; (purchased June, 2011)*


h3. 300234060016190&nbsp; (serial # 122)&nbsp;&nbsp; (both purchased Dec, 2012)


h3. 300234060014550 (serial # 123)

\\

User's Manuals
# [Quick Start Guide v1.2|^Xeos_Melo_manual-1.pdf|quick start]
# [User Manual v1.5|^Melo_User_Manual _watch_circle_V1.5.pdf|Full Manual]
# [Watch Circle Console User Manual v2.1|^Xeos_Melo_manual-3.pdf|watch circle]\\
# [Xeos pricing changes as of Jan 2013|^Xeos_IridiumBillingProcess_CustomerLetter.pdf]]]></property>
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<property name="body"><![CDATA[h4. (as of April, 2015)


h1. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

*21.5m (BAD)*
Now with bad connector...&nbsp;
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos in the attachments of this page.
* late-2014; was this EM cable repaired?

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)

*15.2m (BAD; bad BSR?)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]

\\

All shockles modified Dec 2015 to be like 001 (stretchier cords)

h4. ESP-001 (modified with 'stretchier' cord)

* 44 days during Catalina (April 2014) deployment
* Moran MB deployment (Sep/Oct 2014)
* ECOHAB?
* Del Mar (start May 17, 2016)

h4. ESP-002


h4. ESP-003


h4. ESP-004


h4. ESP-005


h1. Anchor lines

\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4.


h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\
\\]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[h2.


h1. We currently (12-2012) have three Melo trackers

{color:#006600}The Melo is the 'watch-circle' warning transponder for surface moorings.{color}\\

IMEI numbers:

h3. *300034012090780&nbsp; (purchased June, 2011)*


h3. 300234060016190&nbsp; (serial # 122)&nbsp;&nbsp; (both purchased Dec, 2012)


h3. 300234060014550 (serial # 123)

\\

User's Manuals
# [Quick Start Guide v1.2|^Xeos_Melo_manual-1.pdf|quick start]
# [User Manual v1.5|^Melo_User_Manual _watch_circle_V1.5.pdf|Full Manual]
# [Watch Circle Console User Manual v2.1|^Xeos_Melo_manual-3.pdf|watch circle]\\
# [Xeos pricing changes as of Jan 2013|^Xeos_IridiumBillingProcess_CustomerLetter.pdf]]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|2}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[h4. {color:#ff00cc}MAKAI flight w 4 Archives, 1 Lyse-n-go{color}

*Feb 2-4, 2016*

Repeat of Dec flight.&nbsp; Here are notes from Yanwu's summary:

(Note: when reaching each target depth (peak-chl or pre-set), we give Makai 10 minutes to damp down depth undulation.)

Sample#1 (lyse&go sample. At chl peak):
Makai descended from surface, found the chl peak at 8.7m. On the ensuing ascent, Makai held depth at 8.7m, and triggered sample#1.
Took 63 minutes to complete.&nbsp; Then Makai surfaced to "report to shore".

Sample#2 (archive sample. At chl peak):
Makai descended from surface, found the chl peak at 12.7m. On the ensuing ascent, Makai held depth at 12.3m, and triggered sample#2. (Note: the water column was quite mixed vertically. The chl values at 8m and 12m were very close. Makai was doing her best to pick the relatively weak peak.)&nbsp; Took 41 minutes to complete.

Sample#3 (archive sample. At reacquired chl peak):
In order to reacquire the chl peak (considering the peak-chl layer may have moved up or down), Makai intentionally wiggled up and down (up first, then down, and then up). On the "down", it found the chl peak at 13.2m. On the ensuing "up", Makai held depth at 13.0m, and triggered sample#3.&nbsp; Took 40 minutes to complete.

Sample#4 (archive sample. At pre-set 27m. Control sample.):
Makai dove to the pre-set 27m depth, and triggered sample#4.&nbsp; Took 39 minutes to complete.

Sample#5 (archive sample. At pre-set 27m. Control sample.):
Makai stayed at the pre-set 27m depth, and triggered sample#5.&nbsp; Took 38 minutes to complete.

h4. {color:#ff00cc}Del Mar--ESP-Waldo{color}

*May 17, 2016*

Used M/V Merlin (Walt Crampton), with MBARI surface mooring.&nbsp; Divers from SCRIPPS.&nbsp; Deployed with CTD about 400 yds from Del Mar mooring (SE of their mooring). Used new anchor line, #1 shockle, and 35m EM cable.

Ship coordinates when we dropped it:&nbsp; 32' 55.603N&nbsp; 117' 18.895W
Melo coordinates (IMEI: 300034012090780):&nbsp; 32.92633 \-117.31491

Water depth 100m.&nbsp; Divers reported master link at 22.8m, can top at 16.76m.&nbsp; CTD reading \~18m.

Initial mission is to take a sample two hours after sunrise, every weekday. ]]></property>
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<property name="body"><![CDATA[{mockup:Edit_Menu|1}

{mockup:ESP_Menu|1}

As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus

h5. Define/Edit Phases and Protocol Templates

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[{mockup:Phase_Type_Dialog|1}

{mockup:Edit_Menu|1}

{mockup:ESP_Menu|1}

As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus

h5. Define/Edit Phases and Protocol Templates

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[h4. (as of April, 2015)


h1. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.
* del mar 6 month (summer 2016)

*21.5m (BAD)*
Now with bad connector...&nbsp;
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos in the attachments of this page.
* late-2014; was this EM cable repaired?

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)
* Moran deployment (Sept/Oct 2016)

*15.2m (BAD; bad BSR?)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]

\\

All shockles modified Dec 2015 to be like 001 (stretchier cords)

h4. ESP-001 (modified with 'stretchier' cord)

* 44 days during Catalina (April 2014) deployment
* Moran MB deployment (Sep/Oct 2014)
* ECOHAB?
* Del Mar (start May 17, 2016)

h4. ESP-002

* Moran (sep/oct 2016)

h4. ESP-003


h4. ESP-004


h4. ESP-005


h1. Anchor lines

\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4. *57M*

* 2014 Moran deployment in MB
* moran (sep/oct 2016)

h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus

h5. Define/Edit Phases and Protocol Templates

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[h4. (as of April, 2015)


h1. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.
* del mar 6 month (summer 2016)

*21.5m (BAD)*
Now with bad connector...&nbsp;
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos in the attachments of this page.
* late-2014; was this EM cable repaired?

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)
* Moran deployment (Sept/Oct 2016)

*15.2m (BAD; bad BSR?)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]

\\

All shockles modified Dec 2015 to be like 001 (stretchier cords)

h4. ESP-001 (modified with 'stretchier' cord)

* 44 days during Catalina (April 2014) deployment
* Moran MB deployment (Sep/Oct 2014)
* ECOHAB?
* Del Mar (start May 17, 2016)

h4. ESP-002

* Moran (sep/oct 2016)

h4. ESP-003


h4. ESP-004


h4. ESP-005


h1. Anchor lines

\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4. 62m

* moran (sep/oct 2016)

h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\
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<property name="body"><![CDATA[{mockup:ESP_Menu|1}

As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus

h5. Define/Edit Phases and Protocol Templates

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|1}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}



]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}



]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|1}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}



]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|1}

{mockup:EventDetails|1}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}



]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|1}

{mockup:EventDetails|1}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}



]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|2}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|1}

{mockup:EventDetails|1}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}



]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|2}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|1}

{mockup:EventDetails|1}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}



]]></property>
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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* October deployment:
** h6. {color:#ff0099}Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs){color}

h3. Machine Builds

* AIV mounted into Moe
* Elbow still giving problems with sticktion.&nbsp; Cheri and Scott have spent 3 days working on it, yet it still needs 2x the current of the elbow on NEO.&nbsp; Much discussion of what may be the problem.
* Will do a quick can-test this afternoon of NEO with the MFB attached.&nbsp; Will build delrin stand-off to help guide core into can.&nbsp; Addie to talk to Mike P. about this.
* {color:#000000}Dick{color} has checked all Sleepy boards;&nbsp; now needs a host board.&nbsp; Brent will work with Wayne MONDAY to generate a host.&nbsp; Will get to Dick by TUESDAY.&nbsp; Meanwhile, Dick is moving on to testing dwarves.

h3. MFB

* Addie to work on a +mechanical+ solution to the loosening of the mixing stand-pipe.&nbsp; Will not use silicone.
* Will size-test in can this afternoon
* Must connect PCR-module to dwarf via serial cable.&nbsp; Brent has cables; Addie will get and handle config file changes to make it work.
* Delrin stand-offs; talk to Mike P about design.

h3. Software

* Current versions:
** {color:#ff6600}&nbsp;FIRMWARE{color}
*** 2 Dwarf 'flavors':
**** v 2.59--Standard on all dwarves (some dwarves on NEO have 2.58).&nbsp; ALL CORES WILL BE UPGRADED TO 2.59 before October deployment.&nbsp; All dwarves Dick is testing are being loaded with 2.59
**** v.2.59(66Hz)--special version for MFB dwarf
** {color:#ff6600}RUBY{color}
*** Mainline Ruby is on Bruce and Mack
*** A branch is called MFB/NEO--\- this version modifies 3-4 files unique to NEO
** {color:#ff6600}LINUX{color}
*** Mack & Bruce using v1.6---which has slight communications change from NEO.&nbsp; NEO will be upgraded to v1.6 so all running same LINUX.

* Also, a 2nd puck evac added to BAC arrays.&nbsp; Worry is that code is not tested.&nbsp; Chris S. will start testing on Bruce & Mack this weekend.
* Stitching of 'superphase' code will commence early next week (Monday).
* Wayne will work on getting up to speed on our board structure, and set-up a procedure to make board-burning more accessible to the layman.
* Wayne will work on getting firmware into HEX format so easily accesible to all.
* Tracking ESP Boards
** Wayne asked what people wanted to track.&nbsp; He has good idea of variables and will work with technicians to build a MS-Access database to track board builds, and firmware changes on those boards, etc.
* All parts in for antenna installation tomorrow.&nbsp; Scott building a kit for Brent to reterminate cable.&nbsp; Meeting at Abol's house @ 1:00pm.&nbsp; Mounting bracket should be finished by 1 today.
* Tested radio system on Mack.&nbsp; Something wrong because data from buouys can't find the WWW on-ramp..&nbsp; Brent will try and fix this PM; otherwise will work on after antenna installation.

h3. DWSM

* &nbsp;Bell housings should be delivered to MBARI Tuesday.
* Oatmeal can is \~75% finished
* Sphere needed updated drawings--more detail for machining.&nbsp; Doug stopped them from welding holds on the hemisphere and provided ports to hold piece.
* Big purchases coming:&nbsp; Swagloc/Min-K/Electrical fittings
* Must talk about $$ and burn rates in ASTEP/NSF/MBARI
* Doug needs 7 valve-motor mounting parts.&nbsp; Will take from MFB stock, but must re-order/remake.
* Doug has been working on Solidworks assembly drawing for the _Oceanography_ paper.

h3. GUI Development

* Mission GUI.&nbsp; End of next week all compononets should be in mission script GUI.

* Mission state software very expensive, and licensing is labyrinthine.

h3. Other Items:

* Photoshoot of MFB mounted on core will be Tuesday, Sept 23.&nbsp; May mount grill to GG, to minimize impact on team.]]></property>
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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* October deployment:
** h6. {color:#ff0099}Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs){color}

.

h3. Machine Builds

* AIV mounted into Moe
* Elbow still giving problems with sticktion.&nbsp; Cheri and Scott have spent 3 days working on it, yet it still needs 2x the current of the elbow on NEO.&nbsp; Much discussion of what may be the problem.
* Will do a quick can-test this afternoon of NEO with the MFB attached.&nbsp; Will build delrin stand-off to help guide core into can.&nbsp; Addie to talk to Mike P. about this.
* {color:#000000}Dick{color} has checked all Sleepy boards;&nbsp; now needs a host board.&nbsp; Brent will work with Wayne MONDAY to generate a host.&nbsp; Will get to Dick by TUESDAY.&nbsp; Meanwhile, Dick is moving on to testing dwarves.

h3. MFB

* Addie to work on a +mechanical+ solution to the loosening of the mixing stand-pipe.&nbsp; Will not use silicone.
* Will size-test in can this afternoon
* Must connect PCR-module to dwarf via serial cable.&nbsp; Brent has cables; Addie will get and handle config file changes to make it work.
* Delrin stand-offs; talk to Mike P about design.

h3. Software

* Current versions:
** {color:#ff6600}&nbsp;FIRMWARE{color}
*** 2 Dwarf 'flavors':
**** v 2.59--Standard on all dwarves (some dwarves on NEO have 2.58).&nbsp; ALL CORES WILL BE UPGRADED TO 2.59 before October deployment.&nbsp; All dwarves Dick is testing are being loaded with 2.59
**** v.2.59(66Hz)--special version for MFB dwarf
** {color:#ff6600}RUBY{color}
*** Mainline Ruby is on Bruce and Mack
*** A branch is called MFB/NEO--\- this version modifies 3-4 files unique to NEO
** {color:#ff6600}LINUX{color}
*** Mack & Bruce using v1.6---which has slight communications change from NEO.&nbsp; NEO will be upgraded to v1.6 so all running same LINUX.

* Also, a 2nd puck evac added to BAC arrays.&nbsp; Worry is that code is not tested.&nbsp; Chris S. will start testing on Bruce & Mack this weekend.
* Stitching of 'superphase' code will commence early next week (Monday).
* Wayne will work on getting up to speed on our board structure, and set-up a procedure to make board-burning more accessible to the layman.
* Wayne will work on getting firmware into HEX format so easily accesible to all.
* Tracking ESP Boards
** Wayne asked what people wanted to track.&nbsp; He has good idea of variables and will work with technicians to build a MS-Access database to track board builds, and firmware changes on those boards, etc.
* All parts in for antenna installation tomorrow.&nbsp; Scott building a kit for Brent to reterminate cable.&nbsp; Meeting at Abol's house @ 1:00pm.&nbsp; Mounting bracket should be finished by 1 today.
* Tested radio system on Mack.&nbsp; Something wrong because data from buouys can't find the WWW on-ramp..&nbsp; Brent will try and fix this PM; otherwise will work on after antenna installation.

h3. DWSM

* &nbsp;Bell housings should be delivered to MBARI Tuesday.
* Oatmeal can is \~75% finished
* Sphere needed updated drawings--more detail for machining.&nbsp; Doug stopped them from welding holds on the hemisphere and provided ports to hold piece.
* Big purchases coming:&nbsp; Swagloc/Min-K/Electrical fittings
* Must talk about $$ and burn rates in ASTEP/NSF/MBARI
* Doug needs 7 valve-motor mounting parts.&nbsp; Will take from MFB stock, but must re-order/remake.
* Doug has been working on Solidworks assembly drawing for the _Oceanography_ paper.

h3. GUI Development

* Mission GUI.&nbsp; End of next week all compononets should be in mission script GUI.

* Mission state software very expensive, and licensing is labyrinthine.

h3. Other Items:

* Photoshoot of MFB mounted on core will be Tuesday, Sept 23.&nbsp; May mount grill to GG, to minimize impact on team.]]></property>
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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* October deployment:
** h6. {color:#ff0099}Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs){color}

.

h3. Machine Builds

* AIV mounted into Moe
* Elbow still giving problems with sticktion.&nbsp; Cheri and Scott have spent 3 days working on it, yet it still needs 2x the current of the elbow on NEO.&nbsp; Much discussion of what may be the problem.
* Will do a quick can-test this afternoon of NEO with the MFB attached.&nbsp; Will build delrin stand-off to help guide core into can.&nbsp; Addie to talk to Mike P. about this.
* {color:#000000}Dick{color} has checked all Sleepy boards;&nbsp; now needs a host board.&nbsp; Brent will work with Wayne MONDAY to generate a host.&nbsp; Will get to Dick by TUESDAY.&nbsp; Meanwhile, Dick is moving on to testing dwarves.

h3. MFB

* Addie to work on a +mechanical+ solution to the loosening of the mixing stand-pipe.&nbsp; Will not use silicone.
* Will size-test in can this afternoon
* Must connect PCR-module to dwarf via serial cable.&nbsp; Brent has cables; Addie will get and handle config file changes to make it work.
* Delrin stand-offs; talk to Mike P about design.

h3. Software

* Current versions:
* &nbsp;

h3. DWSM

* &nbsp;Bell housings have just been turned, ports cut, and may have to be sent out of state for anodizing.&nbsp; {color:#3300ff}{*}Doug{*}{color} will lean on El Camino...
* 2" Ti plates are here and in queue for cutting into swiss-cheese plates.&nbsp; {color:#3300ff}{*}Jerry/Ray{*}{color} have the drawings for 1 plate; Sample plate drawing (easier) should be finished by next week.
* Oatmeal can is about 20% finished.&nbsp; +Will+ be able to CNC cut the threads on it.
* Several pump parts are here and can be load tested for power draw.
* connectors not ordered but {color:#3300ff}{*}Doug{*}{color} thinks they will be here quickly.
* valves not ordered yet
* complete DWSM instrument will be assembled by end of year.
* Building a high-pressure test interface will cost \~$10K.&nbsp; {color:#3300ff}{*}Doug{*}{color} given advice to charge this to ASTEP, but charge may be split among several funding lines.&nbsp; {color:#3300ff}{*}Jim{*}{color} and {color:#3300ff}{*}Chris S{*}{color}. to meet about this.

h3. GUI Development

* &nbsp;Kevin out sick today, but lots of Confluence activity....

h3. Other Items:

* Diver needs and deployment logistics are still be formulated...
* We are doing well on the calendar (bottom of page)]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 17 July 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2017Jul08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]]]></property>
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h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 17 July 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2017Jul08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|1}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|1}

{mockup:EventDetails|1}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}


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# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|1}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|1}

{mockup:EventDetails|1}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}

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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|1}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|1}

{mockup:EventDetails|1}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}


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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.4|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.4%2004_05_2008.doc]
# [PCR Users Manual v1.0|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20PCR%20Module%20Users%20Manual%20V1.0.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram4-22-08.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h2. Meeting minutes stored in the projectlibrary:&nbsp;

# [Meeting Notes from June 7, 2007|http://oceana.shore.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc]
\\

h2. Meeting minutes stored within Confluence:

# [08nov2007]
# [15Nov2007]
# [29Nov2007]
# [06Dec2007]
# [20Dec2007]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 17 July 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics_worksheet_17JulFeb08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 17 July 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics_worksheet_17JulFeb08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}3G Koa on AKU in Monterey Bay{color}


h6. *Jan 24, 2018*

Deploy Aku with Koa and 60 cartridge archival mission.&nbsp; Collecting \~32 samples for Ed and Kevan (eDNA), then running remainder (~19) as engineering tests with 20 minute filtering time-outs.

h4. {color:#ff00cc}Hawaii MiVEGAS cruise on R/V Falkor{color}

Three ESP instruments delivered:&nbsp; ESP-Koa, MV1, MV2

Three LRAUV were delivered:&nbsp; Opah, Aku, Ahi

They were paired as
Opah-no ESP (just CTD instruments)---during both legs, Opah flew recon in loops around sampling instrument (or tried to).
Aku / Koa
Ahi / MV1
MV2 was installed on bench in Falkor lab

*Leg 1:&nbsp; March 10-22, 2018*

Ahi/MV1 was first to launch (Mar 11), and was pulled under ship and damaged.&nbsp; Recovered \~2 hours later.

Launched Aku/Koa. sampled Mar 17-Mar21.&nbsp; Collected 38 field samples - of those 1 failed - leaked, 1 smeared.

&nbsp;*Leg 2:&nbsp; March 27-Apr 10*

Aku/Koa used again. sampled Mar 28-Apr2.&nbsp; Collected 56 field samples--of those 8 leaked (no sample), 1 smear.

h4. {color:#ff00cc}2G on Yellowstone River{color}

Deployed the following on *July 25, 2018* for full carousel of archives:

ESP-Gordon \-\- Livingston (Carter's Bridge).  45.597148, \-110.566021

ESP-Waldo \-\- Corwin Springs. 45.111612, \-110.793943

&nbsp;Recovered both instruments *Sept 5*.


h4. {color:#ff00cc}3G shakedown in MB for L. Erie{color}

*Aug 2-6, 2018*

First multicartridge L&G flight with SPR in MB.


h4. {color:#ff00cc}3G in L. Erie{color}

*Aug 20-Sept 4, 2018*

We arrived and started building instrument Aug 20.&nbsp; Sent in water Aug 23.&nbsp; Recovered Aug 26 and redeployed 27th.&nbsp; Ran Makai with Koa and 14 L&G cartridges and SPR module; remainder were archival.

h4. {color:#ff00cc}3G Tacklebox in Teton Valley{color}

*Sep 10-12, 2018*

Collected 5 samples (Flat Creek, confluence of Cache/Flat crk, South Park Flat Creek, Fish creek, pond on South Park Flat Creek).&nbsp; tested in situ for E. coli.&nbsp; 3 positives (but Ct's were 36-38, so low copy numbers).\\ \\]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}3G Koa on AKU in Monterey Bay{color}


h6. *Jan 24, 2018*

Deploy Aku with Koa and 60 cartridge archival mission.&nbsp; Collecting \~32 samples for Ed and Kevan (eDNA), then running remainder (~19) as engineering tests with 20 minute filtering time-outs.

h4. {color:#ff00cc}Hawaii MiVEGAS cruise on R/V Falkor{color}

Three ESP instruments delivered:&nbsp; ESP-Koa, MV1, MV2

Three LRAUV were delivered:&nbsp; Opah, Aku, Ahi

They were paired as
Opah-no ESP (just CTD instruments)---during both legs, Opah flew recon in loops around sampling instrument (or tried to).
Aku / Koa
Ahi / MV1
MV2 was installed on bench in Falkor lab

*Leg 1:&nbsp; March 10-22, 2018*

Ahi/MV1 was first to launch (Mar 11), and was pulled under ship and damaged.&nbsp; Recovered \~2 hours later.

Launched Aku/Koa. sampled Mar 17-Mar21.&nbsp; Collected 38 field samples - of those 1 failed - leaked, 1 smeared.

&nbsp;*Leg 2:&nbsp; March 27-Apr 10*

Aku/Koa used again. sampled Mar 28-Apr2.&nbsp; Collected 56 field samples--of those 8 leaked (no sample), 1 smear.

h4. {color:#ff00cc}2G on Yellowstone River{color}

Deployed the following on July 25, 2018 for full carousel of archives:

ESP-Gordon \-\- Livingston (Carter's Bridge).  45.597148, \-110.566021

ESP-Waldo \-\- Corwin Springs. 45.111612, \-110.793943
\\

h4. {color:#ff00cc}3G shakedown in MB for L. Erie{color}

*Aug 2-6, 2018*
\\

h4. {color:#ff00cc}3G in L. Erie{color}

*Aug 20-Sept 4, 2018*

We arrived and started building instrument Aug 20.&nbsp; Sent in water Aug 23.&nbsp; Recovered Aug 26 and redeployed 27th.&nbsp; Ran Makai with Koa and 14 L&G cartridges and SPR module; remainder were archival. ]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}3G Koa on AKU in Monterey Bay{color}


h6. *Jan 24, 2018*

Deploy Aku with Koa and 60 cartridge archival mission.&nbsp; Collecting \~32 samples for Ed and Kevan (eDNA), then running remainder (~19) as engineering tests with 20 minute filtering time-outs.

h4. {color:#ff00cc}Hawaii MiVEGAS cruise on R/V Falkor{color}

Three ESP instruments delivered:&nbsp; ESP-Koa, MV1, MV2

Three LRAUV were delivered:&nbsp; Opah, Aku, Ahi

They were paired as
Opah-no ESP (just CTD instruments)---during both legs, Opah flew recon in loops around sampling instrument (or tried to).
Aku / Koa
Ahi / MV1
MV2 was installed on bench in Falkor lab

*Leg 1:&nbsp; March 10-22, 2018*

Ahi/MV1 was first to launch (Mar 11), and was pulled under ship and damaged.&nbsp; Recovered \~2 hours later.

Launched Aku/Koa. sampled Mar 17-Mar21.&nbsp; Collected 38 field samples - of those 1 failed - leaked, 1 smeared.

&nbsp;*Leg 2:&nbsp; March 27-Apr 10*

Aku/Koa used again. sampled Mar 28-Apr2.&nbsp; Collected 56 field samples--of those 8 leaked (no sample), 1 smear.

h4. {color:#ff00cc}2G on Yellowstone River{color}

Deployed the following on July 25, 2018 for full carousel of archives:


ESP-Gordon \-\- Livingston (Carter's Bridge).  45.597148, \-110.566021

ESP-Waldo \-\- Corwin Springs. 45.111612, \-110.793943
\\

h4. {color:#ff00cc}3G shakedown in MB for L. Erie{color}

*Aug 2-6, 2018*
\\]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}3G Koa on AKU in Monterey Bay{color}


h6. *Jan 24, 2018*

Deploy Aku with Koa and 60 cartridge archival mission.&nbsp; Collecting \~32 samples for Ed and Kevan (eDNA), then running remainder (~19) as engineering tests with 20 minute filtering time-outs.

h4. {color:#ff00cc}Hawaii MiVEGAS cruise on R/V Falkor{color}

&nbsp;Three ESP instruments delivered:&nbsp; ESP-Koa, MV1, MV2

Three LRAUV were delivered:&nbsp; Opah, Aku, Ahi

They were paired as
Opah--no ESP (just CTD instruments)--during both legs, Opah flew recon in loops around sampling instrument (or tried to).
Aku / Koa
Ahi / MV1
MV2 was installed on bench in Falkor lab

*Leg 1:&nbsp; March 10-22, 2018*

Ahi/MV1 was first to launch (Mar 11), and was pulled under ship and damaged.&nbsp; Recovered \~2 hours later.

Launched Aku/Koa. sampled Mar 17-Mar21.&nbsp; Collected 38 field samples--of those 1 failed--leaked, 1 smeared.

&nbsp;*Leg 2:&nbsp; March 27-Apr 10*\\]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}3G Koa on AKU in Monterey Bay{color}



h6. *Jan 24, 2018*

Deploy Aku with Koa and 60 cartridge archival mission.&nbsp; Collecting \~32 samples for Ed and Kevan (eDNA), then running remainder (~19) as engineering tests with 20 minute filtering time-outs. ]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}3G Koa on AKU in Monterey Bay{color}


h6. *Jan 24, 2018*

Deploy Aku with Koa and 60 cartridge archival mission.&nbsp; Collecting \~32 samples for Ed and Kevan (eDNA), then running remainder (~19) as engineering tests with 20 minute filtering time-outs.

h4. {color:#ff00cc}Hawaii MiVEGAS cruise on R/V Falkor{color}

Three ESP instruments delivered:&nbsp; ESP-Koa, MV1, MV2

Three LRAUV were delivered:&nbsp; Opah, Aku, Ahi

They were paired as
Opah-no ESP (just CTD instruments)---during both legs, Opah flew recon in loops around sampling instrument (or tried to).
Aku / Koa
Ahi / MV1
MV2 was installed on bench in Falkor lab

*Leg 1:&nbsp; March 10-22, 2018*

Ahi/MV1 was first to launch (Mar 11), and was pulled under ship and damaged.&nbsp; Recovered \~2 hours later.

Launched Aku/Koa. sampled Mar 17-Mar21.&nbsp; Collected 38 field samples - of those 1 failed - leaked, 1 smeared.

&nbsp;*Leg 2:&nbsp; March 27-Apr 10*

Aku/Koa used again. sampled Mar 28-Apr2.&nbsp; Collected 56 field samples--of those 8 leaked (no sample), 1 smear.

h4. {color:#ff00cc}2G on Yellowstone River{color}

Deployed the following on July 25, 2018

ESP-Gordon \-\- Livingston (Carter's Bridge).  45.597148, \-110.566021

ESP-Waldo \-\- Corwin Springs. 45.111612, \-110.793943
\\

h4. {color:#ff00cc}3G shakedown in MB for L. Erie{color}

*Aug 2-6, 2018*
\\]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}3G Koa on AKU in Monterey Bay{color}


h6. *Jan 24, 2018*

Deploy Aku with Koa and 60 cartridge archival mission.&nbsp; Collecting \~32 samples for Ed and Kevan (eDNA), then running remainder (~19) as engineering tests with 20 minute filtering time-outs.

h4. {color:#ff00cc}Hawaii MiVEGAS cruise on R/V Falkor{color}

Three ESP instruments delivered:&nbsp; ESP-Koa, MV1, MV2

Three LRAUV were delivered:&nbsp; Opah, Aku, Ahi

They were paired as
Opah-no ESP (just CTD instruments)---during both legs, Opah flew recon in loops around sampling instrument (or tried to).
Aku / Koa
Ahi / MV1
MV2 was installed on bench in Falkor lab

*Leg 1:&nbsp; March 10-22, 2018*

Ahi/MV1 was first to launch (Mar 11), and was pulled under ship and damaged.&nbsp; Recovered \~2 hours later.

Launched Aku/Koa. sampled Mar 17-Mar21.&nbsp; Collected 38 field samples\--of those 1 failed-\-leaked, 1 smeared.

&nbsp;*Leg 2:&nbsp; March 27-Apr 10*

Aku/Koa used again. sampled Mar 28-Apr2.&nbsp; Collected 56 field samples--of those 8 leaked (no sample), 1 smear.

h4. {color:#ff00cc}2G on Yellowstone River{color}

Deployed the following on July 25, 2018

ESP-Gordon \-\- Livingston (Carter's Bridge).  45.597148, \-110.566021

ESP-Waldo \-\- Corwin Springs. 45.111612, \-110.793943 \\

h4. {color:#ff00cc}3G shakedown in MB for L. Erie{color}

*Aug 2-6, 2018*\\]]></property>
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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* October deployment:
** Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs).

h3. Machine Builds

* Problems with Mack and Bruce have been resolved since SC visitors.&nbsp; Thanks to work by {color:#3300ff}{*}Scott{*}{color} and {color:#3300ff}{*}Roman{*}{color}.&nbsp; Still noticed forearm slide on Mack needed to hammer each time.&nbsp; This issue should be resolved in next build when we use different slides.
* Still need to mock-up and test new communication protocols to be used during October deployment.&nbsp; {color:#3300ff}{*}Jim{*}{color} will check with Science to see when machines are free for this.
* {color:#3300ff}{*}Scott{*}{color} still working on testing puck sensor boards when he has time.&nbsp; These will not be implemented until after Oct.
* MOE update:&nbsp; easiest to plumb from inside out, and {color:#3300ff}{*}Cheri{*}{color} still waiting on the custom AIV stator cap.&nbsp; Thus, plumbing put aside and she's been building manipulator arm;&nbsp; mechanical work finished, finish wiring today, start testing; hand should be finished early next week.
* 3rd Mooring:&nbsp; all parts are fabbed.&nbsp; {color:#3300ff}{*}jim S{*}{color}. will start building next week or as soon as his immediate FOCE duties are finished.
* {color:#3300ff}{*}Dick{*}{color} checking Sleepy boards, has not started on dwarves yet.&nbsp; As a way to get up to speed, {color:#3300ff}{*}Wayne{*}{color} will insert himself into the QC process of sleepy and dwarf boards.&nbsp; Scott noted that Dick may have jury duty Sep 15/16.

h3. &nbsp;MFB

* {color:#3300ff}{*}Mike P.*{color} has started looking at mounting tombstone (TS) to NEO.&nbsp; Should be mounted by end of next week.
* Grinding noise of ATV was deemed inconsequential.&nbsp; Much discussion about removing detents from valves.
* Sealing around mixing column was discussed.&nbsp; This should be something Chris/Addie/Jim/Scott brainstorm about.
* {color:#3300ff}{*}Addie{*}{color} and {color:#3300ff}{*}Chris P{*}{color}. working on test-plan for MFB/NEO integration.
h3. Software

* Due to Wayne's knee surgery, antenna mounting moved from Sep 6 to either Sept 12 or 13.
** Plan is to make 1 visit.&nbsp; Brent assembling parts necessary and will bring extra router in case we cannot access the one on-site.
* We will clone the 'server' in Brent's office (Bufflehead) to a machine lifted from A244 Lab.&nbsp; Wayne can then use this in his testing of boards.

h3. DWSM

* &nbsp;Bell housings have just been turned, ports cut, and may have to be sent out of state for anodizing.&nbsp; {color:#3300ff}{*}Doug{*}{color} will lean on El Camino...
* 2" Ti plates are here and in queue for cutting into swiss-cheese plates.&nbsp; {color:#3300ff}{*}Jerry/Ray{*}{color} have the drawings for 1 plate; Sample plate drawing (easier) should be finished by next week.
* Oatmeal can is about 20% finished.&nbsp; +Will+ be able to CNC cut the threads on it.
* Several pump parts are here and can be load tested for power draw.
* connectors not ordered but {color:#3300ff}{*}Doug{*}{color} thinks they will be here quickly.
* valves not ordered yet
* complete DWSM instrument will be assembled by end of year.
* Building a high-pressure test interface will cost \~$10K.&nbsp; {color:#3300ff}{*}Doug{*}{color} given advice to charge this to ASTEP, but charge may be split among several funding lines.&nbsp; {color:#3300ff}{*}Jim{*}{color} and {color:#3300ff}{*}Chris S{*}{color}. to meet about this.

h3. GUI Development

* &nbsp;Kevin out sick today, but lots of Confluence activity....

h3. Other Items:

* Diver needs and deployment logistics are still be formulated...
* We are doing well on the [calendar (bottom of page)|ESPAPP:28Aug2008]\]]></property>
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<property name="body"><![CDATA[
# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]]]></property>
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<property name="body"><![CDATA[{mockup:DeploymentDialog|1}


As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|2}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|1}

{mockup:EventDetails|1}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[Doug will be on vacation July 14-July 28.
Scott will be on vacation July 16-July 22.

h2.
present:  Chris S, Addie, Scott, Doug, Brent, Jim

h3. Instrument Builds

* Scott still to start work on ROV mate-able interface.  Will 'interface' with Chad and Marko.
* Dwarf boards on track for a mid-August delivery.
* Mid-October is the Monterey Ocean Experiment (MOE), where we want to deploy Moe w/ PCR.  Our backup plan will be to deploy the tombstone if the grill is not ready.

* Mid-August we will have SC visitors that will want to run Bruce and Mack very hard for two weeks.  Mostly short DA runs.  issues to deal with:
** Bruce collection clamp issue
** Mack hand.  Scott thinks it may just be a rev of the hand (i.e., widening a hole)

* Must remember that Mack and Bruce are still using back-side puck temp sensors.  Neo has been changed to front, as should these two eventually.

h3. MFB

* Still waiting on encoder boards--due early next week.
* gears still to be modified; should be done today
* syringe mount missing two pieces from El Camino order.  Addie checking with Mike.  We may have one set made in-house so as not to wait.
* Will find two dwarf boards for the grill so not to slow Addie.  One must be Rev. 2, Scott looking around for solution.
* Immediate solution to driving the grill will be to use Linux laptop that Bob Herlien has.  Eventually will move to a more portable solution.
* Jim will email Tony asking for another PCR module
* Brent made offer to help with instant Ruby graphing of PCR module data, if/when Addie gets some downtime.

h3. Software

* Much discussion about freeing up ESPShore space.  2 DVD sets and 1HD backup currently exist. _It was decided that files older than July 2006 could be deleted._ Brent and Roman will be the deletors.
* Much discussion about radio link to M0.  Brent has found a private residence that provides beautiful, unobstructed access and has suggested we offer to provide them DSL if we can mount antenna on their house.  Chris S. looking into the legalities and if this would be okay with MBARI.  Stay tuned.

h3. DWSM

* Bell housings at El Camino.  Doug found o-ring problem and has forwarded them a Rev C to work from.
* Swiss Cheese plate will not be finished b/4 vacation.  Maybe EC will make blank and MBARI will do detail work.
* valves not ordered - only a 4-day lead time
* building a fabricated parts list.

h3. Other Items

* ESP running next weeks BBQ.  Jim will organize.  Need 3 cooks/3 cleaners.  Brent has offered a curry rice salad to go with our burgers and famous Costco cookies.]]></property>
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<property name="body"><![CDATA[
As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|2}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|1}

{mockup:EventDetails|1}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* October deployment:
** Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs).

h3. Machine Builds

* Problems with Mack and Bruce have been resolved since SC visitors.&nbsp; Thanks to work by {color:#3300ff}{*}Scott{*}{color} and {color:#3300ff}{*}Roman{*}{color}.&nbsp; Still noticed forearm slide on Mack needed to hammer each time.&nbsp; This issue should be resolved in next build when we use different slides.
* Still need to mock-up and test new communication protocols to be used during October deployment.&nbsp; {color:#3300ff}{*}Jim{*}{color} will check with Science to see when machines are free for this.
* {color:#3300ff}{*}Scott{*}{color} still working on testing puck sensor boards when he has time.&nbsp; These will not be implemented until after Oct.
* MOE update:&nbsp; easiest to plumb from inside out, and {color:#3300ff}{*}Cheri{*}{color} still waiting on the custom AIV stator cap.&nbsp; Thus, plumbing put aside and she's been building manipulator arm;&nbsp; mechanical work finished, finish wiring today, start testing; hand should be finished early next week.
* 3rd Mooring:&nbsp; all parts are fabbed.&nbsp; {color:#3300ff}{*}jim S{*}{color}. will start building next week or as soon as his immediate FOCE duties are finished.
* {color:#3300ff}{*}Dick{*}{color} checking Sleepy boards, has not started on dwarves yet.&nbsp; As a way to get up to speed, {color:#3300ff}{*}Wayne{*}{color} will insert himself into the QC process of sleepy and dwarf boards.&nbsp; Scott noted that Dick may have jury duty Sep 15/16.

h3. &nbsp;MFB

* {color:#3300ff}{*}Mike P.*{color} has started looking at mounting tombstone (TS) to NEO.&nbsp; Should be mounted by end of next week.
* Grinding noise of ATV was deemed inconsequential.&nbsp; Much discussion about removing detents from valves.
* Sealing around mixing column was discussed.&nbsp; This should be something Chris/Addie/Jim/Scott brainstorm about.
* {color:#3300ff}{*}Addie{*}{color} and {color:#3300ff}{*}Chris P{*}{color}. working on test-plan for MFB/NEO integration.
h3. Software

* Due to Wayne's knee surgery, antenna mounting moved from Sep 6 to either Sept 12 or 13.
** Plan is to make 1 visit.&nbsp; Brent assembling parts necessary and will bring extra router in case we cannot access the one on-site.
* We will clone the 'server' in Brent's office (Bufflehead) to a machine lifted from A244 Lab.&nbsp; Wayne can then use this in his testing of boards.

h3. DWSM

* &nbsp;Bell housings have just been turned, ports cut, and may have to be sent out of state for anodizing.&nbsp; {color:#3300ff}{*}Doug{*}{color} will lean on El Camino...
* 2" Ti plates are here and in queue for cutting into swiss-cheese plates.&nbsp; {color:#3300ff}{*}Jerry/Ray{*}{color} have the drawings for 1 plate; Sample plate drawing (easier) should be finished by next week.
* Oatmeal can is about 20% finished.&nbsp; +Will+ be able to CNC cut the threads on it.
* Several pump parts are here and can be load tested for power draw.
* connectors not ordered but {color:#3300ff}{*}Doug{*}{color} thinks they will be here quickly.
* valves not ordered yet
* complete DWSM instrument will be assembled by end of year.
* Building a high-pressure test interface will cost \~$10K.&nbsp; {color:#3300ff}{*}Doug{*}{color} given advice to charge this to ASTEP, but charge may be split among several funding lines.&nbsp; {color:#3300ff}{*}Jim{*}{color} and {color:#3300ff}{*}Chris S{*}{color}. to meet about this.

h3. GUI Development

* &nbsp;Kevin out sick today, but lots of Confluence activity....

h3. Other Items:

* Diver needs and deployment logistics are still be formulated...
* We are doing well on the [calendar (bottom of page)|ESPAPP:28Aug2008]\]]]></property>
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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* October deployment:
** Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs).

h3. Machine Builds

* Problems with Mack and Bruce have been resolved since SC visitors.&nbsp; Thanks to work by {color:#3300ff}{*}Scott{*}{color} and {color:#3300ff}{*}Roman{*}{color}.&nbsp; Still noticed forearm slide on Mack needed to hammer each time.&nbsp; This issue should be resolved in next build when we use different slides.
* Still need to mock-up and test new communication protocols to be used during October deployment.&nbsp; {color:#3300ff}{*}Jim{*}{color} will check with Science to see when machines are free for this.
* {color:#3300ff}{*}Scott{*}{color} still working on testing puck sensor boards when he has time.&nbsp; These will not be implemented until after Oct.
* MOE update:&nbsp; easiest to plumb from inside out, and {color:#3300ff}{*}Cheri{*}{color} still waiting on the custom AIV stator cap.&nbsp; Thus, plumbing put aside and she's been building manipulator arm;&nbsp; mechanical work finished, finish wiring today, start testing; hand should be finished early next week.
* 3rd Mooring:&nbsp; all parts are fabbed.&nbsp; {color:#3300ff}{*}jim S{*}{color}. will start building next week or as soon as his immediate FOCE duties are finished.
* {color:#3300ff}{*}Dick{*}{color} checking Sleepy boards, has not started on dwarves yet.&nbsp; As a way to get up to speed, {color:#3300ff}{*}Wayne{*}{color} will insert himself into the QC process of sleepy and dwarf boards.&nbsp; Scott noted that Dick may have jury duty Sep 15/16.

h3. &nbsp;MFB

* {color:#3300ff}{*}Mike P.*{color} has started looking at mounting tombstone (TS) to NEO.&nbsp; Should be mounted by end of next week.
* Grinding noise of ATV was deemed inconsequential.&nbsp; Much discussion about removing detents from valves.
* Sealing around mixing column was discussed.&nbsp; This should be something Chris/Addie/Jim/Scott brainstorm about.
* {color:#3300ff}{*}Addie{*}{color} and {color:#3300ff}{*}Chris P{*}{color}. working on test-plan for MFB/NEO integration.
h3. Software

* Due to Wayne's knee surgery, antenna mounting moved from Sep 6 to either Sept 12 or 13.
** Plan is to make 1 visit.&nbsp; Brent assembling parts necessary and will bring extra router in case we cannot access the one on-site.
* We will clone the 'server' in Brent's office (Bufflehead) to a machine lifted from A244 Lab.&nbsp; Wayne can then use this in his testing of boards.

h3. DWSM

* &nbsp;Bell housings have just been turned, ports cut, and may have to be sent out of state for anodizing.&nbsp; {color:#3300ff}{*}Doug{*}{color} will lean on El Camino...
* 2" Ti plates are here and in queue for cutting into swiss-cheese plates.&nbsp; {color:#3300ff}{*}Jerry/Ray{*}{color} have the drawings for 1 plate; Sample plate drawing (easier) should be finished by next week.
* Oatmeal can is about 20% finished.&nbsp; +Will+ be able to CNC cut the threads on it.
* Several pump parts are here and can be load tested for power draw.
* connectors not ordered but {color:#3300ff}{*}Doug{*}{color} thinks they will be here quickly.
* valves not ordered yet
* complete DWSM instrument will be assembled by end of year.
* Building a high-pressure test interface will cost \~$10K.&nbsp; {color:#3300ff}{*}Doug{*}{color} given advice to charge this to ASTEP, but charge may be split among several funding lines.&nbsp; {color:#3300ff}{*}Jim{*}{color} and {color:#3300ff}{*}Chris S{*}{color}. to meet about this.

h3. GUI Development

* &nbsp;Kevin out sick today, but lots of Confluence activity....

h3. Other Items:

* Diver needs and deployment logistics are still be formulated...
* We are doing well on the [calendar (bottom of page)|ESPAPP:28Aug2008][]]]></property>
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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* October deployment:
** Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs).

h3. Machine Builds

* Problems with Mack and Bruce have been resolved since SC visitors.&nbsp; Thanks to work by {color:#3300ff}{*}Scott{*}{color} and {color:#3300ff}{*}Roman{*}{color}.&nbsp; Still noticed forearm slide on Mack needed to hammer each time.&nbsp; This issue should be resolved in next build when we use different slides.
* Still need to mock-up and test new communication protocols to be used during October deployment.&nbsp; {color:#3300ff}{*}Jim{*}{color} will check with Science to see when machines are free for this.
* {color:#3300ff}{*}Scott{*}{color} still working on testing puck sensor boards when he has time.&nbsp; These will not be implemented until after Oct.
* MOE update:&nbsp; easiest to plumb from inside out, and {color:#3300ff}{*}Cheri{*}{color} still waiting on the custom AIV stator cap.&nbsp; Thus, plumbing put aside and she's been building manipulator arm;&nbsp; mechanical work finished, finish wiring today, start testing; hand should be finished early next week.
* 3rd Mooring:&nbsp; all parts are fabbed.&nbsp; {color:#3300ff}{*}jim S{*}{color}. will start building next week or as soon as his immediate FOCE duties are finished.
* {color:#3300ff}{*}Dick{*}{color} checking Sleepy boards, has not started on dwarves yet.&nbsp; As a way to get up to speed, {color:#3300ff}{*}Wayne{*}{color} will insert himself into the QC process of sleepy and dwarf boards.&nbsp; Scott noted that Dick may have jury duty Sep 15/16.

h3. &nbsp;MFB

* {color:#3300ff}{*}Mike P.*{color} has started looking at mounting tombstone (TS) to NEO.&nbsp; Should be mounted by end of next week.
* Grinding noise of ATV was deemed inconsequential.&nbsp; Much discussion about removing detents from valves.
* Sealing around mixing column was discussed.&nbsp; This should be something Chris/Addie/Jim/Scott brainstorm about.
* {color:#3300ff}{*}Addie{*}{color} and {color:#3300ff}{*}Chris P{*}{color}. working on test-plan for MFB/NEO integration.
h3. Software

* Due to Wayne's knee surgery, antenna mounting moved from Sep 6 to either Sept 12 or 13.
** Plan is to make 1 visit.&nbsp; Brent assembling parts necessary and will bring extra router in case we cannot access the one on-site.
* We will clone the 'server' in Brent's office (Bufflehead) to a machine lifted from A244 Lab.&nbsp; Wayne can then use this in his testing of boards.

h3. DWSM

* &nbsp;Bell housings have just been turned, ports cut, and may have to be sent out of state for anodizing.&nbsp; {color:#3300ff}{*}Doug{*}{color} will lean on El Camino...
* 2" Ti plates are here and in queue for cutting into swiss-cheese plates.&nbsp; {color:#3300ff}{*}Jerry/Ray{*}{color} have the drawings for 1 plate; Sample plate drawing (easier) should be finished by next week.
* Oatmeal can is about 20% finished.&nbsp; +Will+ be able to CNC cut the threads on it.
* Several pump parts are here and can be load tested for power draw.
* connectors not ordered but {color:#3300ff}{*}Doug{*}{color} thinks they will be here quickly.
* valves not ordered yet
* complete DWSM instrument will be assembled by end of year.
* Building a high-pressure test interface will cost \~$10K.&nbsp; {color:#3300ff}{*}Doug{*}{color} given advice to charge this to ASTEP, but charge may be split among several funding lines.&nbsp; {color:#3300ff}{*}Jim{*}{color} and {color:#3300ff}{*}Chris S{*}{color}. to meet about this.

h3. GUI Development

* &nbsp;Kevin out sick today, but lots of Confluence activity....

h3. Other Items:

* Diver needs and deployment logistics are still be formulated...
* We are doing well on the [calendar (bottom of page)]]]></property>
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<property name="body"><![CDATA[Doug will be on vacation July 14-July 28.
Scott will be on vacation July 16-July 22.

h2.


h3. Instrument Builds

* Scott still to start work on ROV mate-able interface.  Will 'interface' with Chad and Marko.
* Dwarf boards on track for a mid-August delivery.
* mid-October if the Monterey Ocean Experiment (MOE), where we want to deploy Moe w/ PCR.  Our backup plan will be to deploy the tombstone if the grill is not ready.

* Mid-August we will have SC visitors that will want to run Bruce and Mack very hard for two weeks.  Mostly short DA runs.  issues to deal with:
**Bruce collection clamp issue
**Mack hand.  Scott thinks it may just be a rev of the hand (i.e., widening a hole)

* Must remember that Mack and Bruce are still using back-side puck temp sensors.  Neo has been changed to front, as should these two eventually.


h3. MFB

* Still waiting on encoder boards--due early next week.
* gears still to be modified; should be done today
* syringe mount missing two pieces from El Camino order.  Addie checking with Mike.  We may have one set made in-house so as not to wait.
* Will find two dwarf boards for the grill so not to slow Addie.  One must be Rev. 2, Scott looking around for solution.
* Immediate solution to driving the grill will be to use Linux laptop that Bob Herlien has.  Eventually will move to a more portable solution.
* Jim will email Tony asking for another PCR module
* Brent made offer to help with instant Ruby graphing of PCR module data, if/when Addie gets some downtime.


h3. Software

* Much discussion about freeing up ESPShore space.  2 DVD sets and 1HD backup currently exist.  _It was decided that files older than July 2006 could be deleted._ Brent and Roman will be the deletors.
*  Much discussion about radio link to M0.  Brent has found a private residence that provides beautiful, unobstructed access and has suggested we offer to provide them DSL if we can mount antenna on their house.  Chris S. looking into the legalities and if this would be okay with MBARI.  Stay tuned.



h3. DWSM

* Bell housings at El Camino.  Doug found o-ring problem and has forwarded them a Rev C to work from.
* Swiss Cheese plate will not be finished b/4 vacation.  Maybe EC will make blank and MBARI will do detail work.
* valves not ordered - only a 4-day lead time
* building a fabricated parts list.

h3. Other Items

* ESP running next weeks BBQ.  Jim will organize.  Need 3 cooks/3 cleaners.  Brent has offered a curry rice salad to go with our burgers and famous Costco cookies.]]></property>
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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* October deployment:
** Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs).

h3. Machine Builds

* Problems with Mack and Bruce have been resolved since SC visitors.&nbsp; Thanks to work by {color:#3300ff}{*}Scott{*}{color} and {color:#3300ff}{*}Roman{*}{color}.&nbsp; Still noticed forearm slide on Mack needed to hammer each time.&nbsp; This issue should be resolved in next build when we use different slides.
* Still need to mock-up and test new communication protocols to be used during October deployment.&nbsp; {color:#3300ff}{*}Jim{*}{color} will check with Science to see when machines are free for this.
* {color:#3300ff}{*}Scott{*}{color} still working on testing puck sensor boards when he has time.&nbsp; These will not be implemented until after Oct.
* MOE update:&nbsp; easiest to plumb from inside out, and {color:#3300ff}{*}Cheri{*}{color} still waiting on the custom AIV stator cap.&nbsp; Thus, plumbing put aside and she's been building manipulator arm;&nbsp; mechanical work finished, finish wiring today, start testing; hand should be finished early next week.
* 3rd Mooring:&nbsp; all parts are fabbed.&nbsp; {color:#3300ff}{*}jim S{*}{color}. will start building next week or as soon as his immediate FOCE duties are finished.
* {color:#3300ff}{*}Dick{*}{color} checking Sleepy boards, has not started on dwarves yet.&nbsp; As a way to get up to speed, {color:#3300ff}{*}Wayne{*}{color} will insert himself into the QC process of sleepy and dwarf boards.&nbsp; Scott noted that Dick may have jury duty Sep 15/16.

h3. &nbsp;MFB

* {color:#3300ff}{*}Mike P.*{color} has started looking at mounting tombstone (TS) to NEO.&nbsp; Should be mounted by end of next week.
* Grinding noise of ATV was deemed inconsequential.&nbsp; Much discussion about removing detents from valves.
* Sealing around mixing column was discussed.&nbsp; This should be something Chris/Addie/Jim/Scott brainstorm about.
* {color:#3300ff}{*}Addie{*}{color} and {color:#3300ff}{*}Chris P{*}{color}. working on test-plan for MFB/NEO integration.
h3. Software

* Due to Wayne's knee surgery, antenna mounting moved from Sep 6 to either Sept 12 or 13.
** Plan is to make 1 visit.&nbsp; Brent assembling parts necessary and will bring extra router in case we cannot access the one on-site.
* We will clone the 'server' in Brent's office (Bufflehead) to a machine lifted from A244 Lab.&nbsp; Wayne can then use this in his testing of boards.

h3. DWSM

* &nbsp;Bell housings have just been turned, ports cut, and may have to be sent out of state for anodizing.&nbsp; {color:#3300ff}{*}Doug{*}{color} will lean on El Camino...
* 2" Ti plates are here and in queue for cutting into swiss-cheese plates.&nbsp; {color:#3300ff}{*}Jerry/Ray{*}{color} have the drawings for 1 plate; Sample plate drawing (easier) should be finished by next week.
* Oatmeal can is about 20% finished.&nbsp; +Will+ be able to CNC cut the threads on it.
* Several pump parts are here and can be load tested for power draw.
* connectors not ordered but {color:#3300ff}{*}Doug{*}{color} thinks they will be here quickly.
* valves not ordered yet
* complete DWSM instrument will be assembled by end of year.
* Building a high-pressure test interface will cost \~$10K.&nbsp; {color:#3300ff}{*}Doug{*}{color} given advice to charge this to ASTEP, but charge may be split among several funding lines.&nbsp; {color:#3300ff}{*}Jim{*}{color} and {color:#3300ff}{*}Chris S{*}{color}. to meet about this.

h3. GUI Development

* &nbsp;Kevin out sick today, but lots of Confluence activity....

h3. Other Items:

* Diver needs and deployment logistics are still be formulated...]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]
# 04Sep2008]]></property>
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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* October deployment:
** Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs).

h3. Machine Builds

* Puck sensor boards (10 made) have been modified and {color:#0000ff}{*}Scott{*}{color}is still testing on GG in the fridge.&nbsp; Will fit in as fridge schedule opens up.
* Mack giving many problems to SC group, who leave tomorrow.&nbsp; {color:#3300ff}{*}Chris{*}{color} thinks its a PBV calbration problem.&nbsp; Intermittent.&nbsp; Scott will start tackling this on Tuesday.
* Syringe testing:&nbsp; not really time-critical.&nbsp; Will perform after October deployment.&nbsp; {color:#3300ff}{*}Scott{*}{color} also wants to test on syringe frames in the cold.&nbsp; Still waiting on delivery of 10ml CS.
* {color:#3300ff}{*}Dick{*}{color} checking Dwarfs and R-valve boards.

h3. &nbsp;MFB

* Tombstone (TS) has worked in the cold.&nbsp; Now re-doing at ambient to compare.
* There was a never-before-seen error in the driver data from the module;&nbsp; maybe the module burped data that Ruby couldn't handle or it could be a threading issue.&nbsp; Bob Herlien is being contacted about this problem.
* Bracket to hold PCR module on grill will be ready Tues/Weds next week
* All syringe speeds on TS are working with voltage regulator on syringe and rotary valves (not heaters).
* Have noticed the gains on the grill syringe are much different than those on the TS, probably due to plunger/syringe tightness differences.&nbsp; Means Grill uses more power than TS.
* Seal on mixing column still not good.&nbsp; New o-rings ordered, will come in Tuesday.&nbsp; {color:#3300ff}{*}Addie{*}{color} to buy PEEK tubing cutter.
* Stand-Alone power boards are not critical path yet, so {color:#3300ff}{*}Scott{*}{color} will wait until after deployment.
* {color:#3300ff}{*}Addie{*}{color} and {color:#3300ff}{*}Chris P{*}{color}. need to come up with a test plan for the TS/Grill for mounting on a&nbsp; core.
* {color:#3300ff}{*}Addie{*}{color} will let {color:#3300ff}{*}Mike P.*{color} know that we are mounting TS on Neo for October; mike should start the physical mount Sept 9-11.

h3.


h3. Software

* Limit switch code is now working.&nbsp; Small slight tweaking needed, but pretty much finished.
* Mack's brain freeze; stuck doing a single Ruby primitive.&nbsp; We killed process and started again.&nbsp; Will look for it to happen again.
* Upon looking at antenna house,&nbsp; {color:#0000ff}{*}Brent{*}{color} and {color:#3300ff}{*}Wayne{*}{color} are making slight changes to antenna location.&nbsp; We want to 'kit' the installation so there will only be 1 visit.&nbsp; Brent continues to try and setup the router/antenna.&nbsp;

h3. DWSM

* &nbsp;{color:#0000ff}{*}Doug{*}{color} found that bell housing still not finished; next week.&nbsp; Then it will be sent to another shop for Ni-acetate anodizing (sliver was color decided on).
* much discussion about anodizing to slow galvanic corrosion; Sphere is too large to anodize so perhaps use a polyurethane spray.
* Critical Path for DWSM is the swiss cheese plates.&nbsp; Plans have been given to Ray & Jerry who think they can do it.&nbsp; Must check with them for a timeline.
* Soup can is now a 2-piece Oatmeal can, which we are doing in-house.
* {color:#3300ff}{*}Scott{*}{color} still to order connectors in and out of DWSM housing.
* Doug explained the possible testing procedures of DWSM in his email:{color:#006600}There are two pressure modes and three assembly options.{color}
{color:#006600}&nbsp;{color}
{color:#006600}Running modes are: ASME rated (aka safe to stand next to) and Exclusion (put in pressure test facility and run remotely){color}
{color:#006600}Assembly modes are: 3/8" SS internal screws and open HP motor, 3/8 screws and closed HP motor, or B7 jacket bolts. The HP pump shaft seal has low pressure limit, hence the need for the compensated motor. The jacket bolting needs the complete closed housing assembly, MINK's cables, etc.{color}
&nbsp;
|| || ASME Rated || Exclusion ||
| 3/8 Screws, open HP motor | \~10 psi | \- |
| 3/8 Screws, closed HP motor | 220 psi \\ | 550 psi \\ |
| 7/8 B7 Jacket | 1500 psi | 5885 psi |
{color:#006600}This means that we do need the soup can housing to do any significant development, but that we can run the full cycle (at reduced pressure) before fully terminatingeverything. The soup can is in the machine shop queue along with a lot of other parts that we need.{color}
&nbsp;
* Scott suggested we go ahead and rent a Freezer van to both test the sphere at temp, and use as a pressure test housing for the DWSM.&nbsp; will look into.
* {color:#3300ff}{*}Scott{*}{color} to order connectors that go in and out of DWSM housing.
* Doug to order normal Swageloc SS fittings and test corrosive properties against Ti plate.
* Quote of the day:
** "Nothing on DWSM will be effected by the cold."&nbsp; \--Douglas Pargett 8-28-2008 11:48am ;-)

h3. GUI Development

* &nbsp;Kevin making changes to GUI in time for Oct deployment
* Will be finished by Sept 26.
* Still trying to get an evaluation version of machine state software.

h3. Other Items:

Invited paper to Oceanography is due Sept 15.&nbsp; Chris will need help with some figures.
{gliffy:name=Oct deploy calendar|space=ESPAPP|page=28Aug2008|pageid=6259023|align=left|size=L}]]></property>
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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* October deployment:
** Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs).

h3. Machine Builds

* Puck sensor boards (10 made) have been modified and {color:#0000ff}{*}Scott{*}{color}is still testing on GG in the fridge.&nbsp; Will fit in as fridge schedule opens up.
* Mack giving many problems to SC group, who leave tomorrow.&nbsp; {color:#3300ff}{*}Chris{*}{color} thinks its a PBV calbration problem.&nbsp; Intermittent.&nbsp; Scott will start tackling this on Tuesday.
* Syringe testing:&nbsp; not really time-critical.&nbsp; Will perform after October deployment.&nbsp; {color:#3300ff}{*}Scott{*}{color} also wants to test on syringe frames in the cold.&nbsp; Still waiting on delivery of 10ml CS.
* {color:#3300ff}{*}Dick{*}{color} checking Dwarfs and R-valve boards.

h3. &nbsp;MFB

* Tombstone (TS) has worked in the cold.&nbsp; Now re-doing at ambient to compare.
* There was a never-before-seen error in the driver data from the module;&nbsp; maybe the module burped data that Ruby couldn't handle or it could be a threading issue.&nbsp; Bob Herlien is being contacted about this problem.
* Bracket to hold PCR module on grill will be ready Tues/Weds next week
* All syringe speeds on TS are working with voltage regulator on syringe and rotary valves (not heaters).
* Have noticed the gains on the grill syringe are much different than those on the TS, probably due to plunger/syringe tightness differences.&nbsp; Means Grill uses more power than TS.
* Seal on mixing column still not good.&nbsp; New o-rings ordered, will come in Tuesday.&nbsp; {color:#3300ff}{*}Addie{*}{color} to buy PEEK tubing cutter.
* Stand-Alone power boards are not critical path yet, so {color:#3300ff}{*}Scott{*}{color} will wait until after deployment.
* {color:#3300ff}{*}Addie{*}{color} and {color:#3300ff}{*}Chris P{*}{color}. need to come up with a test plan for the TS/Grill for mounting on a&nbsp; core.
* {color:#3300ff}{*}Addie{*}{color} will let {color:#3300ff}{*}Mike P.*{color} know that we are mounting TS on Neo for October; mike should start the physical mount Sept 9-11.

h3.


h3. Software

* Limit switch code is now working.&nbsp; Small slight tweaking needed, but pretty much finished.
* Mack's brain freeze; stuck doing a single Ruby primitive.&nbsp; We killed process and started again.&nbsp; Will look for it to happen again.
* Upon looking at antenna house,&nbsp; {color:#0000ff}{*}Brent{*}{color} and {color:#3300ff}{*}Wayne{*}{color} are making slight changes to antenna location.&nbsp; We want to 'kit' the installation so there will only be 1 visit.&nbsp; Brent continues to try and setup the router/antenna.&nbsp;

h3. DWSM

* &nbsp;{color:#0000ff}{*}Doug{*}{color} found that bell housing still not finished; next week.&nbsp; Then it will be sent to another shop for Ni-acetate anodizing (sliver was color decided on).
* much discussion about anodizing to slow galvanic corrosion; Sphere is too large to anodize so perhaps use a polyurethane spray.
* Critical Path for DWSM is the swiss cheese plates.&nbsp; Plans have been given to Ray & Jerry who think they can do it.&nbsp; Must check with them for a timeline.
* Soup can is now a 2-piece Oatmeal can, which we are doing in-house.
* {color:#3300ff}{*}Scott{*}{color} still to order connectors in and out of DWSM housing.
* Doug explained the possible testing procedures of DWSM in his email:{color:#006600}There are two pressure modes and three assembly options.{color}
{color:#006600}&nbsp;{color}
{color:#006600}Running modes are: ASME rated (aka safe to stand next to) and Exclusion (put in pressure test facility and run remotely){color}
{color:#006600}Assembly modes are: 3/8" SS internal screws and open HP motor, 3/8 screws and closed HP motor, or B7 jacket bolts. The HP pump shaft seal has low pressure limit, hence the need for the compensated motor. The jacket bolting needs the complete closed housing assembly, MINK's cables, etc.{color}
&nbsp;
|| || ASME Rated || Exclusion ||
| 3/8 Screws, open HP motor | ~10 psi | \- |
| 3/8 Screws, closed HP motor | 220 psi\\ | 550 psi\\ |
| 7/8 B7 Jacket | 1500 psi | 5885 psi |{color:#006600}This means that we do need the soup can housing to do any significant development, but that we can run the full cycle (at reduced pressure) before fully terminating everything. The soup can is in the machine shop queue along with a lot of other parts that we need.{color}
&nbsp;]]></property>
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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* October deployment:
** Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs).

h3. Machine Builds

* Puck sensor boards (10 made) have been modified and {color:#0000ff}{*}Scott{*}{color}is still testing on GG in the fridge.&nbsp; Will fit in as fridge schedule opens up.
* Mack giving many problems to SC group, who leave tomorrow.&nbsp; {color:#3300ff}{*}Chris{*}{color} thinks its a PBV calbration problem.&nbsp; Intermittent.&nbsp; Scott will start tackling this on Tuesday.
* Syringe testing:&nbsp; not really time-critical.&nbsp; Will perform after October deployment.&nbsp; {color:#3300ff}{*}Scott{*}{color} also wants to test on syringe frames in the cold.&nbsp; Still waiting on delivery of 10ml CS.
* {color:#3300ff}{*}Dick{*}{color} checking Dwarfs and R-valve boards.

h3. &nbsp;MFB

* Tombstone (TS) has worked in the cold.&nbsp; Now re-doing at ambient to compare.
* There was a never-before-seen error in the driver data from the module;&nbsp; maybe the module burped data that Ruby couldn't handle or it could be a threading issue.&nbsp; Bob Herlien is being contacted about this problem.
* Bracket to hold PCR module on grill will be ready Tues/Weds next week
* All syringe speeds on TS are working with voltage regulator on syringe and rotary valves (not heaters).
* Have noticed the gains on the grill syringe are much different than those on the TS, probably due to plunger/syringe tightness differences.&nbsp; Means Grill uses more power than TS.
* Seal on mixing column still not good.&nbsp; New o-rings ordered, will come in Tuesday.&nbsp; {color:#3300ff}{*}Addie{*}{color} to buy PEEK tubing cutter.
* Stand-Alone power boards are not critical path yet, so {color:#3300ff}{*}Scott{*}{color} will wait until after deployment.
* {color:#3300ff}{*}Addie{*}{color} and {color:#3300ff}{*}Chris P{*}{color}. need to come up with a test plan for the TS/Grill for mounting on a&nbsp; core.
* {color:#3300ff}{*}Addie{*}{color} will let {color:#3300ff}{*}Mike P.*{color} know that we are mounting TS on Neo for October; mike should start the physical mount Sept 9-11.

h3.


h3. Software

* Limit switch code is now working.&nbsp; Small slight tweaking needed, but pretty much finished.
* Mack's brain freeze; stuck doing a single Ruby primitive.&nbsp; We killed process and started again.&nbsp; Will look for it to happen again.
* Upon looking at antenna house,&nbsp; {color:#0000ff}{*}Brent{*}{color} and {color:#3300ff}{*}Wayne{*}{color} are making slight changes to antenna location.&nbsp; We want to 'kit' the installation so there will only be 1 visit.&nbsp; Brent continues to try and setup the router/antenna.&nbsp;

h3. DWSM

* &nbsp;{color:#0000ff}{*}Doug{*}{color} found that bell housing still not finished; next week.&nbsp; Then it will be sent to another shop for Ni-acetate anodizing (sliver was color decided on).
* much discussion about anodizing to slow galvanic corrosion; Sphere is too large to anodize so perhaps use a polyurethane spray.
* Critical Path for DWSM is the swiss cheese plates.&nbsp; Plans have been given to Ray & Jerry who think they can do it.&nbsp; Must check with them for a timeline.
* Soup can is now a 2-piece Oatmeal can, which we are doing in-house.
* {color:#3300ff}{*}Scott{*}{color} still to order connectors in and out of DWSM housing.
* Doug explained the possible testing procedures of DWSM in his email:{color:#006600}There are two pressure modes and three assembly options.{color}
{color:#006600}&nbsp;{color}
{color:#006600}Running modes are: ASME rated (aka safe to stand next to) and Exclusion (put in pressure test facility and run remotely){color}
{color:#006600}Assembly modes are: 3/8" SS internal screws and open HP motor, 3/8 screws and closed HP motor, or B7 jacket bolts. The HP pump shaft seal has low pressure limit, hence the need for the compensated motor. The jacket bolting needs the complete closed housing assembly, MINK's cables, etc.{color}
&nbsp;
|| || ASME Rated || Exclusion ||
| 3/8 Screws, open HP motor | \~10 psi | \- |
| 3/8 Screws, closed HP motor | 220 psi \\ | 550 psi \\ |
| 7/8 B7 Jacket | 1500 psi | 5885 psi |
{color:#006600}This means that we do need the soup can housing to do any significant development, but that we can run the full cycle (at reduced pressure) before fully terminatingeverything. The soup can is in the machine shop queue along with a lot of other parts that we need.{color}
&nbsp;
* Scott suggested we go ahead and rent a Freezer van to both test the sphere at temp, and use as a pressure test housing for the DWSM.&nbsp; will look into.
* {color:#3300ff}{*}Scott{*}{color} to order connectors that go in and out of DWSM housing.
* Doug to order normal Swageloc SS fittings and test corrosive properties against Ti plate.
* Quote of the day:
** "Nothing on DWSM will be effected by the cold."&nbsp; \--Douglas Pargett 8-28-2008 11:48am ;-)

h3. GUI Development

* &nbsp;Kevin making changes to GUI in time for Oct deployment
* Will be finished by Sept 26.
* Still trying to get an evaluation version of machine state software.

h3. Other Items:

Invited paper to Oceanography is due Sept 15.&nbsp; Chris will need help with some figures.]]></property>
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<property name="body"><![CDATA[{mockup:InstrumentDialog|1}

As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|2}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|1}

{mockup:EventDetails|1}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|2}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|1}

{mockup:EventDetails|1}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|2}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|1}

{mockup:EventDetails|1}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[h3. Schedule Items&nbsp;

* October deployment:
** Using Shanna Rae;&nbsp; MOB on October 8 (Weds), deploy October 9 (Thurs).

h3. Machine Builds

* Puck sensor boards (10 made) have been modified and {color:#0000ff}{*}Scott{*}{color}is still testing on GG in the fridge.&nbsp; Will fit in as fridge schedule opens up.
* Mack giving many problems to SC group, who leave tomorrow.&nbsp; {color:#3300ff}{*}Chris{*}{color} thinks its a PBV calbration problem.&nbsp; Intermittent.&nbsp; Scott will start tackling this on Tuesday.
* Syringe testing:&nbsp; not really time-critical.&nbsp; Will perform after October deployment.&nbsp; {color:#3300ff}{*}Scott{*}{color} also wants to test on syringe frames in the cold.&nbsp; Still waiting on delivery of 10ml CS.
* {color:#3300ff}{*}Dick{*}{color} checking Dwarfs and R-valve boards.

h3. &nbsp;MFB

* Tombstone (TS) has worked in the cold.&nbsp; Now re-doing at ambient to compare.
* There was a never-before-seen error in the driver data from the module;&nbsp; maybe the module burped data that Ruby couldn't handle or it could be a threading issue.&nbsp; Bob Herlien is being contacted about this problem.
* Bracket to hold PCR module on grill will be ready Tues/Weds next week
* All syringe speeds on TS are working with voltage regulator on syringe and rotary valves (not heaters).
* Have noticed the gains on the grill syringe are much different than those on the TS, probably due to plunger/syringe tightness differences.&nbsp; Means Grill uses more power than TS.
* Seal on mixing column still not good.&nbsp; New o-rings ordered, will come in Tuesday.&nbsp; {color:#3300ff}{*}Addie{*}{color} to buy PEEK tubing cutter.
* Stand-Alone power boards are not critical path yet, so {color:#3300ff}{*}Scott{*}{color} will wait until after deployment.
* {color:#3300ff}{*}Addie{*}{color} and {color:#3300ff}{*}Chris P{*}{color}. need to come up with a test plan for the TS/Grill for mounting on a&nbsp; core.
* {color:#3300ff}{*}Addie{*}{color} will let {color:#3300ff}{*}Mike P.*{color} know that we are mounting TS on Neo for October; mike should start the physical mount Sept 9-11.

h3.


h3. Software

* Limit switch code is now working.&nbsp; Small slight tweaking needed, but pretty much finished.
* Mack's brain freeze; stuck doing a single Ruby primitive.&nbsp; We killed process and started again.&nbsp; Will look for it to happen again.
* Upon looking at antenna house,&nbsp; {color:#0000ff}{*}Brent{*}{color} and {color:#3300ff}{*}Wayne{*}{color} are making slight changes to antenna location.&nbsp; We want to 'kit' the installation so there will only be 1 visit.&nbsp; Brent continues to try and setup the router/antenna.&nbsp;

h3. DWSM

* &nbsp;{color:#0000ff}{*}Doug{*}{color} found that bell housing still not finished; next week.&nbsp; Then it will be sent to another shop for Ni-acetate anodizing (sliver was color decided on).
* much discussion about anodizing to slow galvanic corrosion; Sphere is too large to anodize so perhaps use a polyurethane spray.
* Critical Path for DWSM is the swiss cheese plates.&nbsp; Plans have been given to Ray & Jerry who think they can do it.&nbsp; Must check with them for a timeline.
* Soup can is now a 2-piece Oatmeal can, which we are doing in-house.
* {color:#3300ff}{*}Scott{*}{color} still to order connectors in and out of DWSM housing.
* Doug explained the possible testing procedures of DWSM in his email:{color:#006600}There are two pressure modes and three assembly options.{color}
{color:#006600}&nbsp;{color}
{color:#006600}Running modes are: ASME rated (aka safe to stand next to) and Exclusion (put in pressure test facility and run remotely){color}
{color:#006600}Assembly modes are: 3/8" SS internal screws and open HP motor, 3/8 screws and closed HP motor, or B7 jacket bolts. The HP pump shaft seal has low pressure limit, hence the need for the compensated motor. The jacket bolting needs the complete closed housing assembly, MINK's cables, etc.{color}
&nbsp;
|| || ASME Rated || Exclusion ||
| 3/8 Screws, open HP motor | \~10 psi | \- |
| 3/8 Screws, closed HP motor | 220 psi \\ | 550 psi \\ |
| 7/8 B7 Jacket | 1500 psi | 5885 psi |
{color:#006600}This means that we do need the soup can housing to do any significant development, but that we can run the full cycle (at reduced pressure) before fully terminatingeverything. The soup can is in the machine shop queue along with a lot of other parts that we need.{color}
&nbsp;
* Scott suggested we go ahead and rent a Freezer van to both test the sphere at temp, and use as a pressure test housing for the DWSM.&nbsp; will look into.
* {color:#3300ff}{*}Scott{*}{color} to order connectors that go in and out of DWSM housing.
* Doug to order normal Swageloc SS fittings and test corrosive properties against Ti plate.
* Quote of the day:
** "Nothing on DWSM will be effected by the cold."&nbsp; \--Douglas Pargett 8-28-2008 11:48am ;-)

h3. GUI Development

* &nbsp;Kevin making changes to GUI in time for Oct deployment
* Will be finished by Sept 26.
* Still trying to get an evaluation version of machine state software.

h3. Other Items:

Invited paper to Oceanography is due Sept 15.&nbsp; Chris will need help with some figures.\\

Project Calendar for Sept/Oct:

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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|11}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|2}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|2}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|1}

{mockup:EventDetails|1}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|1}

{mockup:ConsumedResources|1}

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|1}

{mockup:InstrumentState|1}


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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| | G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| 1 \\ | Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| 2 | Intake point and Screen \\ | | | | 2 |
| 3 | | | | | |
| 4 | Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| 5 | Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| 6 | Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| 7 | Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| 8 | Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| 9 | Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| 10 | Filter selection valving \\
(transition from sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| 11 | Cartridge Seals \\ | | | | 2 |
| 12 | \\ | | | | |
| 13 | \\ | \\ | \\ | | |
| 14 | Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| 15 | Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| 16 | Filter Evacuate \\ | * Need to remove seawater <5% of lysis volume.
* In G2, remaining seawater needs to be <100uL
* For 1mL lysis volume, <50uL, or <1 drop.
** Test numbers: Dry filter \+holder, 9.91g
** wet filter (filter holder dry) 9.95g (40 uL)
** no change if vacuumed, no change w/ singe 10ml blow thru
** after 3X 10mL blow thru, 9.92g (10 uL)
** filter appeared to be mostly dry | * Air pressure evac (G2 method)
* Vacuum assist below filter?
* Filter holder is piston assembly, w/ small dead volumes
* Displacement with other fluid? | | 4 |
| 17 | Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| 18 | DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| 19 | Direct Capture \\ | | | | |
| 20 | Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| 21 | Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| 22 | | | | | |
| 23 | Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| 24 | Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| 25 | Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| 26 | Cartridge Actuators \\ | | | | 4 |
| 27 | \\ | \\ | \\ | \\ | |
| 28 | Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| 29 | Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| 30 | | | | | |
| 31 | TRANSFER TO AM | | | | |
| 32 | Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| 33 | AM Selector Injection Loop \\ | | | | 4 \\ |
| 34 | Clean Injection Loop \\ | | | | 4 \\ |
| 35 | Rotor Pass-Thru \\ | | | | 2 |
| 36 | LRAUV Platform Interface \\ | | | | 2 \\ |
| 37 | LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | See model \\
G3LRAUVHousing.sldasm \\ | 2 \\ |
| 38 | | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| | G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| 1 \\ | Ambient Flush Reservoir \\ | * Mixtures, chemicals?
* Volume (s)
* Material compatibility
* Dilution with SW?
* Flush fluids as well? | | \\ | 1 |
| 2 | Intake point and Screen \\ | * Single intake?
* CU screens?
* Location on LRAUV
* Min bore size? | | | 2 |
| 3 | | | | | |
| 4 | Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * Number of ports (intakes and ambient storage)?
* 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| 5 | Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| 6 | Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| 7 | Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| 8 | Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| 9 | Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| 10 | Filter selection valving \\
(transition from sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| 11 | Cartridge Seals \\ | | | | 2 |
| 12 | \\ | | | | |
| 13 | \\ | \\ | \\ | | |
| 14 | Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| 15 | Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| 16 | Filter Evacuate \\ | * Need to remove seawater <5% of lysis volume.
* In G2, remaining seawater needs to be <100uL
* For 1mL lysis volume, <50uL, or <1 drop.
** Test numbers: Dry filter \+holder, 9.91g
** wet filter (filter holder dry) 9.95g (40 uL)
** no change if vacuumed, no change w/ singe 10ml blow thru
** after 3X 10mL blow thru, 9.92g (10 uL)
** filter appeared to be mostly dry | * Air pressure evac (G2 method)
* Vacuum assist below filter?
* Filter holder is piston assembly, w/ small dead volumes
* Displacement with other fluid? | | 4 |
| 17 | Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| 18 | DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| 19 | Direct Capture \\ | | | | |
| 20 | Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| 21 | Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| 22 | | | | | |
| 23 | Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| 24 | Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| 25 | Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| 26 | Cartridge Actuators \\ | | | | 4 |
| 27 | \\ | \\ | \\ | \\ | |
| 28 | Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| 29 | Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| 30 | | | | | |
| 31 | TRANSFER TO AM | | | | |
| 32 | Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| 33 | AM Selector Injection Loop \\ | | | | 4 \\ |
| 34 | Clean Injection Loop \\ | | | | 4 \\ |
| 35 | Rotor Pass-Thru \\ | | | | 2 |
| 36 | LRAUV Platform Interface \\ | | | | 2 \\ |
| 37 | LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | See model \\
G3LRAUVHousing.sldasm \\ | 2 \\ |
| 38 | | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| | G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| 1 \\ | Ambient Flush Reservoir \\ | * Mixtures, chemicals?
* Volume (s)
* Material compatibility
* Dilution with SW?
* Flush fluids as well? | | \\ | 1 |
| 2 | Intake point and Screen \\ | * Single intake?
* CU screens?
* Location on LRAUV
* Min bore size? | | | 2 |
| 3 | | | | | |
| 4 | Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * Number of ports (intakes and ambient storage)?
* 3-way valve
* Min bore size?
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| 5 | Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi
* Min bore size?
* Non-corroding
* Fail closed
* Wattage? Power budget?
* Small scale, Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| 6 | Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* Min bore size?
* low power
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| 7 | Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| 8 | Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| 9 | Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| 10 | Filter selection valving \\
(transition from sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| 11 | Cartridge Seals \\ | | | | 2 |
| 12 | \\ | | | | |
| 13 | \\ | \\ | \\ | | |
| 14 | Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| 15 | Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| 16 | Filter Evacuate \\ | * Need to remove seawater <5% of lysis volume.
* In G2, remaining seawater needs to be <100uL
* For 1mL lysis volume, <50uL, or <1 drop.
** Test numbers: Dry filter \+holder, 9.91g
** wet filter (filter holder dry) 9.95g (40 uL)
** no change if vacuumed, no change w/ singe 10ml blow thru
** after 3X 10mL blow thru, 9.92g (10 uL)
** filter appeared to be mostly dry | * Air pressure evac (G2 method)
* Vacuum assist below filter?
* Filter holder is piston assembly, w/ small dead volumes
* Displacement with other fluid? | | 4 |
| 17 | Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| 18 | DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| 19 | Direct Capture \\ | | | | |
| 20 | Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| 21 | Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| 22 | | | | | |
| 23 | Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| 24 | Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| 25 | Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| 26 | Cartridge Actuators \\ | | | | 4 |
| 27 | \\ | \\ | \\ | \\ | |
| 28 | Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| 29 | Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| 30 | | | | | |
| 31 | TRANSFER TO AM | | | | |
| 32 | Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| 33 | AM Selector Injection Loop \\ | | | | 4 \\ |
| 34 | Clean Injection Loop \\ | | | | 4 \\ |
| 35 | Rotor Pass-Thru \\ | | | | 2 |
| 36 | LRAUV Platform Interface \\ | | | | 2 \\ |
| 37 | LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | See model \\
G3LRAUVHousing.sldasm \\ | 2 \\ |
| 38 | | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[h3. Deployment Update

* All three instrument working well.&nbsp; Problem with Neo's radio was that it was running on low power.&nbsp; Trip to mooring allowed this to change.&nbsp; Santa Cruz radio link was spotty; Brent thinks that the mooring is 100 yards too far east forcing signal to traverse lots of land.&nbsp; A minor tweak of his roof antenna has made transfer speeds acceptable.
* Neo has had 1 error; elevator retry while moving pucks; doesn't look serious.
* Message rules need to be reviewed; phone emails of bad news are not getting sent.&nbsp; Scott and Brent to work on this.

h3. Machine Builds

* MOE:&nbsp; temperature mounts made and now on
* elbow and harmonic drive still problematic.&nbsp; Many hours by many people spent to get drive aligned but no luck.&nbsp; Going to plan B:
** order 2-axle (pre-aligned) harmonic drive and redesign mount on arm
** use GG's arm to finish build and calibrating of Moe.&nbsp; Cheri estimates 2 weeks and it will be ready to hand to science.
* Cheri working on BOM for the two ASTEP II instruments to be built in 2009.
* El Camino has delivered a small number of parts for the next two units

h3. MFB

\\

h3. Software

* Starlight Xpress, our camera manufacturer can still get old USB boards, but upon recalculation, we may not need them for 2009.&nbsp; Currently we have 4 USB 1.1 cameras:&nbsp; Doucette, Scholin lab, spare, and GG's. We could purchase and trade 2 newer cameras for Doucette and Scholin lab, and have 4 older cameras available.&nbsp; Would still like a price for Starlight to make the old ones, but now no rush.
* Brent arranged a visit from a board manufacturer with ties to LabView.&nbsp; Invited interested parties.
* &nbsp;

h3. DWSM


h5. Sphere

Doug made Tapemation visit on Tuesday:
** Sphere bottom looks good.&nbsp; Lathing finished, now onto mill; should be finished ~ 2 weeks.
** Top still an issue.&nbsp; Doug re-did drawings to try and adjust to the poor casting.&nbsp; Top will need minor machining (lift points, and thru-holes to connect to bottom)
** Pictures of these are in project Library.&nbsp; Check out&nbsp;&nbsp; ESP/DWSM/4k DWSM/4k Sphere Pictures/4k Sphere machining

h5. DWSM

* &nbsp;Will be built in Bldg. B lab
* Must build a test-rig for filtering oil
* Bulkhead plates (swiss cheese) have finished face-machining.&nbsp; Now doing sides of plates.&nbsp; Looks like Ray will finish before he goes on vacation.
* Doug ready for Dwarf/host/sleepy combo to start testing subassemblies.
* Syntactic foam to arrive in January.&nbsp; Currently enough foam for 12 batteries, which is out contingent weight (if stuff is heavier than calculated, we will have to remove some batteries, lessening deployment time.)
* Preliminary elevator idea has been vetted with Lobos crew.&nbsp; Preliminary dimensions and weights will work.

h3. GUI Development


h3. Other Items:]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| | G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| 1 \\ | Ambient Flush Reservoir \\ | * Mixtures, chemicals?
* Volume (s)
* Material compatibility
* Dilution with SW?
* Flush fluids as well? | | \\ | 1 |
| 2 | Intake point and Screen \\ | * Single intake?
* CU screens?
* Location on LRAUV
* Min bore size? | | | 2 |
| 3 | | | | | |
| 4 | Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * Number of ports (intakes and ambient storage)?
* 3-way valve
* Min bore size?
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| 5 | Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi
* Min bore size?
* Non-corroding
* Fail closed
* Wattage? Power budget?
* Small scale, Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| 6 | Cartridge Selection valves \\ | * Chemical suitable
* 500 psi
* Min bore size?
* low power
* flush free | * Ladder/Looper options
* 2 position spool valves
* Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| 7 | Cartridge Return Array \\ | | * check valve
* part of Selection valve
*  | * LeeCo
* Parker | 4 |
| 8 | Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| 9 | Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| 10 | Filter selection valving \\
(transition from sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| 11 | Cartridge Seals \\ | | | | 2 |
| 12 | \\ | | | | |
| 13 | \\ | \\ | \\ | | |
| 14 | Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| 15 | Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| 16 | Filter Evacuate \\ | * Need to remove seawater <5% of lysis volume.
* In G2, remaining seawater needs to be <100uL
* For 1mL lysis volume, <50uL, or <1 drop.
** Test numbers: Dry filter \+holder, 9.91g
** wet filter (filter holder dry) 9.95g (40 uL)
** no change if vacuumed, no change w/ singe 10ml blow thru
** after 3X 10mL blow thru, 9.92g (10 uL)
** filter appeared to be mostly dry | * Air pressure evac (G2 method)
* Vacuum assist below filter?
* Filter holder is piston assembly, w/ small dead volumes
* Displacement with other fluid? | | 4 |
| 17 | Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| 18 | DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| 19 | Direct Capture \\ | | | | |
| 20 | Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| 21 | Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| 22 | | | | | |
| 23 | Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| 24 | Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| 25 | Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| 26 | Cartridge Actuators \\ | | | | 4 |
| 27 | \\ | \\ | \\ | \\ | |
| 28 | Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| 29 | Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| 30 | | | | | |
| 31 | TRANSFER TO AM | | | | |
| 32 | Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| 33 | AM Selector Injection Loop \\ | | | | 4 \\ |
| 34 | Clean Injection Loop \\ | | | | 4 \\ |
| 35 | Rotor Pass-Thru \\ | | | | 2 |
| 36 | LRAUV Platform Interface \\ | | | | 2 \\ |
| 37 | LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | See model \\
G3LRAUVHousing.sldasm \\ | 2 \\ |
| 38 | | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[h3. Deployment Update


h3. Machine Builds
\\

h3. MFB
\\

h3. Software
\\

h3. DWSM
\\

h3. GUI Development


h3. Other Items:]]></property>
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<property name="body"><![CDATA[h3. Deployment Update

* All three instrument working well.&nbsp; Problem with Neo's radio was that it was running on low power.&nbsp; Trip to mooring allowed this to change.&nbsp; Santa Cruz radio link was spotty; Brent thinks that the mooring is 100 yards too far east forcing signal to traverse lots of land.&nbsp; A minor tweak of his roof antenna has made transfer speeds acceptable.
* Neo has had 1 error; elevator retry while moving pucks; doesn't look serious.
* Message rules need to be reviewed; phone emails of bad news are not getting sent.&nbsp; Scott and Brent to work on this.

h3. Machine Builds

* MOE:&nbsp; temperature mounts made and now on
* elbow and harmonic drive still problematic.&nbsp; Many hours by many people spent to get drive aligned but no luck.&nbsp; Going to plan B:
** order 2-axle (pre-aligned) harmonic drive and redesign mount on arm
** use GG's arm to finish build and calibrating of Moe.&nbsp; Cheri estimates 2 weeks and it will be ready to hand to science.
* Cheri working on BOM for the two ASTEP II instruments to be built in 2009.
* El Camino has delivered a small number of parts for the next two units

h3. MFB

* Parts list for 3 ASTEP II MFB's and remaining parts for current 7 MFB's will be finished early next week.&nbsp; Plan is to send jobs to a Santa Cruz shop since El Camino is overbooked.
\\

h3. Software

* Starlight Xpress, our camera manufacturer can still get old USB boards, but upon recalculation, we may not need them for 2009.&nbsp; Currently we have 4 USB 1.1 cameras:&nbsp; Doucette, Scholin lab, spare, and GG's. We could purchase and trade 2 newer cameras for Doucette and Scholin lab, and have 4 older cameras available.&nbsp; Would still like a price for Starlight to make the old ones, but now no rush.
* Brent arranged a visit from a board manufacturer with ties to LabView.&nbsp; Invited interested parties.
* h6. &nbsp;DWARF ISSUES:

** Wayne has found you can take a good board, but when trying to clone bits from it, we can't identify the processor.&nbsp; Much discussion on why this may be; perhaps blown fuse?
** Writing of Dwarf Novella;&nbsp; {color:#3300ff}{*}Brent & Wayne to meet Monday 2-4pm{*}{color} to discuss this.
** Wayne building a Verilog motion-control test bench for Scott.
** Cloning of Bufflehead:&nbsp; {color:#ff0000}{*}Friday, 1:00pm start of clone{*}{color}.

h3. DWSM


h5. Sphere

Doug made Tapemation visit on Tuesday:
** Sphere bottom looks good.&nbsp; Lathing finished, now onto mill; should be finished ~ 2 weeks.
** Top still an issue.&nbsp; Doug re-did drawings to try and adjust to the poor casting.&nbsp; Top will need minor machining (lift points, and thru-holes to connect to bottom)
** Pictures of these are in project Library.&nbsp; Check out [http://mww.mbari.org/projectlibrary/ESP/DWSM/4k%DWSM/4k%Sphere%Pictures/4k%Sphere%machining]

Meeting Notes from June 7, 2007|http://mww.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc]\\

h5. DWSM

* &nbsp;Will be built in Bldg. B lab
* Must build a test-rig for filtering oil
* Bulkhead plates (swiss cheese) have finished face-machining.&nbsp; Now doing sides of plates.&nbsp; Looks like Ray will finish before he goes on vacation.
* Doug ready for Dwarf/host/sleepy combo to start testing subassemblies.
* Syntactic foam to arrive in January.&nbsp; Currently enough foam for 12 batteries, which is out contingent weight (if stuff is heavier than calculated, we will have to remove some batteries, lessening deployment time.)
* Preliminary elevator idea has been vetted with Lobos crew.&nbsp; Preliminary dimensions and weights will work.

h3. GUI Development


h3. Other Items:]]></property>
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<property name="body"><![CDATA[h3. Deployment Update

* All three instrument working well.&nbsp; Problem with Neo's radio was that it was running on low power.&nbsp; Trip to mooring allowed this to change.&nbsp; Santa Cruz radio link was spotty; Brent thinks that the mooring is 100 yards too far east forcing signal to traverse lots of land.&nbsp; A minor tweak of his roof antenna has made transfer speeds acceptable.
* Neo has had 1 error; elevator retry while moving pucks; doesn't look serious.
* Message rules need to be reviewed; phone emails of bad news are not getting sent.&nbsp; Scott and Brent to work on this.

h3. Machine Builds

* MOE:&nbsp; temperature mounts made and now on
* elbow and harmonic drive still problematic.&nbsp; Many hours by many people spent to get drive aligned but no luck.&nbsp; Going to plan B:
** order 2-axle (pre-aligned) harmonic drive and redesign mount on arm
** use GG's arm to finish build and calibrating of Moe.&nbsp; Cheri estimates 2 weeks and it will be ready to hand to science.
* Cheri working on BOM for the two ASTEP II instruments to be built in 2009.
* El Camino has delivered a small number of parts for the next two units

h3. MFB

* Parts list for 3 ASTEP II MFB's and remaining parts for current 7 MFB's will be finished early next week.&nbsp; Plan is to send jobs to a Santa Cruz shop since El Camino is overbooked.
\\

h3. Software

* Starlight Xpress, our camera manufacturer can still get old USB boards, but upon recalculation, we may not need them for 2009.&nbsp; Currently we have 4 USB 1.1 cameras:&nbsp; Doucette, Scholin lab, spare, and GG's. We could purchase and trade 2 newer cameras for Doucette and Scholin lab, and have 4 older cameras available.&nbsp; Would still like a price for Starlight to make the old ones, but now no rush.
* Brent arranged a visit from a board manufacturer with ties to LabView.&nbsp; Invited interested parties.
* h6. &nbsp;DWARF ISSUES:

** Wayne has found you can take a good board, but when trying to clone bits from it, we can't identify the processor.&nbsp; Much discussion on why this may be; perhaps blown fuse?
** Writing of Dwarf Novella;&nbsp; {color:#3300ff}{*}Brent & Wayne to meet Monday 2-4pm{*}{color} to discuss this.
** Wayne building a Verilog motion-control test bench for Scott.
** Cloning of Bufflehead:&nbsp; {color:#ff0000}{*}Friday, 1:00pm start of clone{*}{color}.

h3. DWSM


h5. Sphere

Doug made Tapemation visit on Tuesday:
** Sphere bottom looks good.&nbsp; Lathing finished, now onto mill; should be finished ~ 2 weeks.
** Top still an issue.&nbsp; Doug re-did drawings to try and adjust to the poor casting.&nbsp; Top will need minor machining (lift points, and thru-holes to connect to bottom)
** Pictures of these are in project Library.&nbsp; Check out [http://mww.mbari.org/projectlibrary/ESP/DWSM/4k DWSM/4k Sphere Pictures/4k Sphere machining]

Meeting Notes from June 7, 2007\|http://mww.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc\]
\\

h5. DWSM

* &nbsp;Will be built in Bldg. B lab
* Must build a test-rig for filtering oil
* Bulkhead plates (swiss cheese) have finished face-machining.&nbsp; Now doing sides of plates.&nbsp; Looks like Ray will finish before he goes on vacation.
* Doug ready for Dwarf/host/sleepy combo to start testing subassemblies.
* Syntactic foam to arrive in January.&nbsp; Currently enough foam for 12 batteries, which is out contingent weight (if stuff is heavier than calculated, we will have to remove some batteries, lessening deployment time.)
* Preliminary elevator idea has been vetted with Lobos crew.&nbsp; Preliminary dimensions and weights will work.

h3. GUI Development


h3. Other Items:]]></property>
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<property name="body"><![CDATA[h3. Deployment Update

* All three instrument working well.&nbsp; Problem with Neo's radio was that it was running on low power.&nbsp; Trip to mooring allowed this to change.&nbsp; Santa Cruz radio link was spotty; Brent thinks that the mooring is 100 yards too far east forcing signal to traverse lots of land.&nbsp; A minor tweak of his roof antenna has made transfer speeds acceptable.
* Neo has had 1 error; elevator retry while moving pucks; doesn't look serious.
* Message rules need to be reviewed; phone emails of bad news are not getting sent.&nbsp; Scott and Brent to work on this.

h3. Machine Builds

* MOE:&nbsp; temperature mounts made and now on
* elbow and harmonic drive still problematic.&nbsp; Many hours by many people spent to get drive aligned but no luck.&nbsp; Going to plan B:
** order 2-axle (pre-aligned) harmonic drive and redesign mount on arm
** use GG's arm to finish build and calibrating of Moe.&nbsp; Cheri estimates 2 weeks and it will be ready to hand to science.
* Cheri working on BOM for the two ASTEP II instruments to be built in 2009.
* El Camino has delivered a small number of parts for the next two units

h3. MFB

* Parts list for 3 ASTEP II MFB's and remaining parts for current 7 MFB's will be finished early next week.&nbsp; Plan is to send jobs to a Santa Cruz shop since El Camino is overbooked.
\\

h3. Software

* Starlight Xpress, our camera manufacturer can still get old USB boards, but upon recalculation, we may not need them for 2009.&nbsp; Currently we have 4 USB 1.1 cameras:&nbsp; Doucette, Scholin lab, spare, and GG's. We could purchase and trade 2 newer cameras for Doucette and Scholin lab, and have 4 older cameras available.&nbsp; Would still like a price for Starlight to make the old ones, but now no rush.
* Brent arranged a visit from a board manufacturer with ties to LabView.&nbsp; Invited interested parties.
* h6. &nbsp;DWARF ISSUES:

** Wayne has found you can take a good board, but when trying to clone bits from it, we can't identify the processor.&nbsp; Much discussion on why this may be; perhaps blown fuse?
** Writing of Dwarf Novella;&nbsp; {color:#3300ff}{*}Brent & Wayne to meet Monday 2-4pm{*}{color} to discuss this.
** Wayne building a Verilog motion-control test bench for Scott.
** Cloning of Bufflehead:&nbsp; {color:#ff0000}{*}Friday, 1:00pm start of clone{*}{color}.

h3. DWSM


h5. Sphere

Doug made Tapemation visit on Tuesday:
** Sphere bottom looks good.&nbsp; Lathing finished, now onto mill; should be finished ~ 2 weeks.
** Top still an issue.&nbsp; Doug re-did drawings to try and adjust to the poor casting.&nbsp; Top will need minor machining (lift points, and thru-holes to connect to bottom)
** Pictures of these are in project Library.&nbsp; Check out&nbsp;&nbsp; ESP/DWSM/4k DWSM/4k Sphere Pictures/4k Sphere machining

h5. DWSM

* &nbsp;Will be built in Bldg. B lab
* Must build a test-rig for filtering oil
* Bulkhead plates (swiss cheese) have finished face-machining.&nbsp; Now doing sides of plates.&nbsp; Looks like Ray will finish before he goes on vacation.
* Doug ready for Dwarf/host/sleepy combo to start testing subassemblies.
* Syntactic foam to arrive in January.&nbsp; Currently enough foam for 12 batteries, which is out contingent weight (if stuff is heavier than calculated, we will have to remove some batteries, lessening deployment time.)
* Preliminary elevator idea has been vetted with Lobos crew.&nbsp; Preliminary dimensions and weights will work.

h3. GUI Development


h3. Other Items:]]></property>
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<property name="body"><![CDATA[h2. Overview

h2. Notes

The printer used by [~scholin] is a custom printer. It can not output GAL files. It does put out a text file that I'm trying to parse and work with. A copy of the file is checked into [SVN|http://kahuna.shore.mbari.org/viewvc.cgi/esp/trunk/esp-imaging/src/test/resources/imaging/2_22_08comptest_2008-02-25_142348_Run.txt?view=markup].

h3. Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:
{noformat}
SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK
{noformat}

_SpotX_ and _SpotY_ are coordinates in micrometers starting in the upper left hand corner of the paper. The _0, 0_ point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out.

_SrcWell_ indicates the contents of the spots. For example, all spots from the _C-1_ source well will have identical chemistries applied.

h3. Image Analysis

Maximum Entropy thresholding does a decent job of delineating the control spots. Unfortunately, I haven't found a technique for delineating the spots that don't go off. In fact those spots can contain values within the range of the background noise. 

{gallery}

h4. Possible avenues of exploration

The ESP folks would like an automated image analysis package that:
# Reads the image
# locates the spots (either with or without the help of the GAL-like file)
# Read the highest 8x8 block (full size image) or 4x4 block (half-size image) average within the spot. The block average is square with no weighting applied.
# Return a text file (Tab or comma delimited) with:
#* Average intensity associated with the _SrcWell_ (i.e. C-1, A-1, etc.)
#* Standard deviation by _SrcWell_
#* Average intensity of background disk (excluding spot values)


h3. References
# Old ESP Matlab toolbox at [http://moonjelly/cgi-bin/cvsweb.cgi/ESP/matlab/]
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<property name="body"><![CDATA[h3. Deployment Update

* All three instrument working well.&nbsp; Problem with Neo's radio was that it was running on low power.&nbsp; Trip to mooring allowed this to change.&nbsp; Santa Cruz radio link was spotty; Brent thinks that the mooring is 100 yards too far east forcing signal to traverse lots of land.&nbsp; A minor tweak of his roof antenna has made transfer speeds acceptable.
* Neo has had 1 error; elevator retry while moving pucks; doesn't look serious.
* Message rules need to be reviewed; phone emails of bad news are not getting sent.&nbsp; Scott and Brent to work on this.

h3. Machine Builds

* MOE:&nbsp; temperature mounts made and now on
* elbow and harmonic drive still problematic.&nbsp; Many hours by many people spent to get drive aligned but no luck.&nbsp; Going to plan B:
** order 2-axle (pre-aligned) harmonic drive and redesign mount on arm
** use GG's arm to finish build and calibrating of Moe.&nbsp; Cheri estimates 2 weeks and it will be ready to hand to science.
* Cheri working on BOM for the two ASTEP II instruments to be built in 2009.
* El Camino has delivered a small number of parts for the next two units

h3. MFB

* Parts list for 3 ASTEP II MFB's and remaining parts for current 7 MFB's will be finished early next week.&nbsp; Plan is to send jobs to a Santa Cruz shop since El Camino is overbooked.
\\

h3. Software

* Starlight Xpress, our camera manufacturer can still get old USB boards, but upon recalculation, we may not need them for 2009.&nbsp; Currently we have 4 USB 1.1 cameras:&nbsp; Doucette, Scholin lab, spare, and GG's. We could purchase and trade 2 newer cameras for Doucette and Scholin lab, and have 4 older cameras available.&nbsp; Would still like a price for Starlight to make the old ones, but now no rush.
* Brent arranged a visit from a board manufacturer with ties to LabView.&nbsp; Invited interested parties.
* h6. &nbsp;DWARF ISSUES:

** Wayne has found you can take a good board, but when trying to clone bits from it, we can't identify the processor.&nbsp; Much discussion on why this may be; perhaps blown fuse?
** Writing of Dwarf Novella;&nbsp; {color:#3300ff}{*}Brent & Wayne to meet Monday 2-4pm{*}{color} to discuss this.
** Wayne building a Verilog motion-control test bench for Scott.
** Cloning of Bufflehead:&nbsp; {color:#ff0000}{*}Friday, 1:00pm start of clone{*}{color}.

h3. DWSM


h5. Sphere

Doug made Tapemation visit on Tuesday:
** Sphere bottom looks good.&nbsp; Lathing finished, now onto mill; should be finished ~ 2 weeks.
** Top still an issue.&nbsp; Doug re-did drawings to try and adjust to the poor casting.&nbsp; Top will need minor machining (lift points, and thru-holes to connect to bottom)
** Pictures of these are in project Library.&nbsp; Check out&nbsp;&nbsp; [cifs://tornado.shore.mbari.org/projectlibrary/ESP/DWSM/4k DWSM/4k Sphere Pictures/4k Sphere machining]

h5. DWSM

* &nbsp;Will be built in Bldg. B lab
* Must build a test-rig for filtering oil
* Bulkhead plates (swiss cheese) have finished face-machining.&nbsp; Now doing sides of plates.&nbsp; Looks like Ray will finish before he goes on vacation.
* Doug ready for Dwarf/host/sleepy combo to start testing subassemblies.
* Syntactic foam to arrive in January.&nbsp; Currently enough foam for 12 batteries, which is out contingent weight (if stuff is heavier than calculated, we will have to remove some batteries, lessening deployment time.)
* Preliminary elevator idea has been vetted with Lobos crew.&nbsp; Preliminary dimensions and weights will work.

h3. GUI Development


h3. Other Items:]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2019Feb08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# Frit Identification system

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science]]></property>
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<property name="body"><![CDATA[h3. Deployment Update

* All three instrument working well.&nbsp; Problem with Neo's radio was that it was running on low power.&nbsp; Trip to mooring allowed this to change.&nbsp; Santa Cruz radio link was spotty; Brent thinks that the mooring is 100 yards too far east forcing signal to traverse lots of land.&nbsp; A minor tweak of his roof antenna has made transfer speeds acceptable.
* Neo has had 1 error; elevator retry while moving pucks; doesn't look serious.
* Message rules need to be reviewed; phone emails of bad news are not getting sent.&nbsp; Scott and Brent to work on this.

h3. Machine Builds

* MOE:&nbsp; temperature mounts made and now on
* elbow and harmonic drive still problematic.&nbsp; Many hours by many people spent to get drive aligned but no luck.&nbsp; Going to plan B:
** order 2-axle (pre-aligned) harmonic drive and redesign mount on arm
** use GG's arm to finish build and calibrating of Moe.&nbsp; Cheri estimates 2 weeks and it will be ready to hand to science.
* Cheri working on BOM for the two ASTEP II instruments to be built in 2009.
* El Camino has delivered a small number of parts for the next two units

h3. MFB

* Parts list for 3 ASTEP II MFB's and remaining parts for current 7 MFB's will be finished early next week.&nbsp; Plan is to send jobs to a Santa Cruz shop since El Camino is overbooked.
\\

h3. Software

* Starlight Xpress, our camera manufacturer can still get old USB boards, but upon recalculation, we may not need them for 2009.&nbsp; Currently we have 4 USB 1.1 cameras:&nbsp; Doucette, Scholin lab, spare, and GG's. We could purchase and trade 2 newer cameras for Doucette and Scholin lab, and have 4 older cameras available.&nbsp; Would still like a price for Starlight to make the old ones, but now no rush.
* Brent arranged a visit from a board manufacturer with ties to LabView.&nbsp; Invited interested parties.
* h6. &nbsp;DWARF ISSUES:

** Wayne has found you can take a good board, but when trying to clone bits from it, we can't identify the processor.&nbsp; Much discussion on why this may be; perhaps blown fuse?
** Writing of Dwarf Novella;&nbsp; {color:#3300ff}{*}Brent & Wayne to meet Monday 2-4pm{*}{color} to discuss this.
** Wayne building a Verilog motion-control test bench for Scott.
** Cloning of Bufflehead:&nbsp; {color:#ff0000}{*}Friday, 1:00pm start of clone{*}{color}.

h3. DWSM


h5. Sphere

Doug made Tapemation visit on Tuesday:
** Sphere bottom looks good.&nbsp; Lathing finished, now onto mill; should be finished ~ 2 weeks.
** Top still an issue.&nbsp; Doug re-did drawings to try and adjust to the poor casting.&nbsp; Top will need minor machining (lift points, and thru-holes to connect to bottom)
** Pictures of these are in project Library.&nbsp; Check out /projectlibrary/ESP/DWSM/4k DWSM/4k Sphere Pictures/4k Sphere machining

h5. DWSM

* &nbsp;Will be built in Bldg. B lab
* Must build a test-rig for filtering oil
* Bulkhead plates (swiss cheese) have finished face-machining.&nbsp; Now doing sides of plates.&nbsp; Looks like Ray will finish before he goes on vacation.
* Doug ready for Dwarf/host/sleepy combo to start testing subassemblies.
* Syntactic foam to arrive in January.&nbsp; Currently enough foam for 12 batteries, which is out contingent weight (if stuff is heavier than calculated, we will have to remove some batteries, lessening deployment time.)
* Preliminary elevator idea has been vetted with Lobos crew.&nbsp; Preliminary dimensions and weights will work.

h3. GUI Development


h3. Other Items:]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram (updated 19 Feb 2008) |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2019Feb08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science]]></property>
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<property name="body"><![CDATA[h3. Deployment Update

* All three instrument working well.&nbsp; Problem with Neo's radio was that it was running on low power.&nbsp; Trip to mooring allowed this to change.&nbsp; Santa Cruz radio link was spotty; Brent thinks that the mooring is 100 yards too far east forcing signal to traverse lots of land.&nbsp; A minor tweak of his roof antenna has made transfer speeds acceptable.
* Neo has had 1 error; elevator retry while moving pucks; doesn't look serious.
* Message rules need to be reviewed; phone emails of bad news are not getting sent.&nbsp; Scott and Brent to work on this.

h3. Machine Builds

* MOE:&nbsp; temperature mounts made and now on
* elbow and harmonic drive still problematic.&nbsp; Many hours by many people spent to get drive aligned but no luck.&nbsp; Going to plan B:
** order 2-axle (pre-aligned) harmonic drive and redesign mount on arm
** use GG's arm to finish build and calibrating of Moe.&nbsp; Cheri estimates 2 weeks and it will be ready to hand to science.
* Cheri working on BOM for the two ASTEP II instruments to be built in 2009.
* El Camino has delivered a small number of parts for the next two units

h3. MFB

* Parts list for 3 ASTEP II MFB's and remaining parts for current 7 MFB's will be finished early next week.&nbsp; Plan is to send jobs to a Santa Cruz shop since El Camino is overbooked.
\\

h3. Software

* Starlight Xpress, our camera manufacturer can still get old USB boards, but upon recalculation, we may not need them for 2009.&nbsp; Currently we have 4 USB 1.1 cameras:&nbsp; Doucette, Scholin lab, spare, and GG's. We could purchase and trade 2 newer cameras for Doucette and Scholin lab, and have 4 older cameras available.&nbsp; Would still like a price for Starlight to make the old ones, but now no rush.
* Brent arranged a visit from a board manufacturer with ties to LabView.&nbsp; Invited interested parties.
* h6. &nbsp;DWARF ISSUES:

** Wayne has found you can take a good board, but when trying to clone bits from it, we can't identify the processor.&nbsp; Much discussion on why this may be; perhaps blown fuse?
** Writing of Dwarf Novella;&nbsp; {color:#3300ff}{*}Brent & Wayne to meet Monday 2-4pm{*}{color} to discuss this.
** Wayne building a Verilog motion-control test bench for Scott.
** Cloning of Bufflehead:&nbsp; {color:#ff0000}{*}Friday, 1:00pm start of clone{*}{color}.

h3. DWSM


h5. Sphere

Doug made Tapemation visit on Tuesday:
** Sphere bottom looks good.&nbsp; Lathing finished, now onto mill; should be finished ~ 2 weeks.
** Top still an issue.&nbsp; Doug re-did drawings to try and adjust to the poor casting.&nbsp; Top will need minor machining (lift points, and thru-holes to connect to bottom)
** Pictures of these are in project Library.&nbsp; Check out [http://mww.mbari.org/projectlibrary/ESP/DWSM/4k DWSM/4k Sphere Pictures/4k Sphere machining]

h5. DWSM

* &nbsp;Will be built in Bldg. B lab
* Must build a test-rig for filtering oil
* Bulkhead plates (swiss cheese) have finished face-machining.&nbsp; Now doing sides of plates.&nbsp; Looks like Ray will finish before he goes on vacation.
* Doug ready for Dwarf/host/sleepy combo to start testing subassemblies.
* Syntactic foam to arrive in January.&nbsp; Currently enough foam for 12 batteries, which is out contingent weight (if stuff is heavier than calculated, we will have to remove some batteries, lessening deployment time.)
* Preliminary elevator idea has been vetted with Lobos crew.&nbsp; Preliminary dimensions and weights will work.

h3. GUI Development


h3. Other Items:]]></property>
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<property name="body"><![CDATA[h2. Notes

[~brian]: Here's a [UML of the current data model | ^ESP - Data Model UML.pdf]. A few things to note:

* I color coded classes by related groups. Cascading transactions work within related groups only, e.g. deleting an instrument will delete all the associated yellow classes only. I haven't tested out all the Cascade relations yet, so deleting an image might delete your instrument to :-). These should be easy fixes but I won't be able to write the tests until after my vacation sometime about 7/16.
* I've written a basic CRUD test so I know that it can insert and delete trees of objects. Beyond that we'll have to work things out.
* At this point there is NO buisness logic implemented.  If a transaction breaks some database rule, for example, trying to insert a ConsumableAmount without a ConsumableType, an Exception will be thrown.
* Collections are lazy loaded but I haven't written any unit tests to verify that they're working.
* I had some issues with the ConsumableAmount table. It's a many-to-many join table with an extra column for storing a value. JPA *hates* that. (You have to have the primary keys for both the ConsumableType and PhaseType *BEFORE* inserting the ConsumableAmount; so ConsumableAmount would've need to be handled is separate transactions.) The workaround was to add an id column; it's not pretty but it works. 
* All testing has been done against FOG. Is this copacetic or should I start setting up MySQL for developing against?
* All transactions are currently handled through a single EAO object.
* The ESP-DAL (<- Data Access Layer) build uses Maven 2. A dependency graph is available at [here | ^ESP - Data Model Dependencies.png]

Kevin: Some questions I have about the model
* What sort of things go in Event_Types?  I think we are using those for mostly stuff that gets parsed out of the log file and stuffed into events, but should we have Protocol_Run, Phases, or Deployments in the event types even though they are actually subclasses?
* I think the Eventt hierarchy should look like Deployment->Phases->Protocol_Runs.  Just want to verify.]]></property>
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h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 15 Sep 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2015Sep08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 15 Sep 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2015Sep08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# Radio Communication commands for tri-deployment (10-7-08)
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]]]></property>
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# [10Jan2008]
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# [24Jan2008]
# [31Jan2008]
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# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]
# [04Sep2008]
# [11Sep2008]
# [18Sep2008]
# [25Sep2008]
# [02Oct2008] (Pre-deployment discussions)]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15-18, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;

h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 27\- May 8, 2017*

This was part of a 5-vehicle launch (Tethys, Daphne, Aku w/ ESP Honu, Ahi, Opah).&nbsp; Gabe Foreman arrived from UH to help with piloting.&nbsp; Adam Jones helped launch Aku and Opah.

Ran multiple simulation to test the mission.

On Weds, May 3, tried first 'real' concurrent sampling.&nbsp; Cartridge 1 threw an alignment error--could not push on plunge valve.&nbsp; We labeled that cartridge 'wet' and moved to cartridge 2.&nbsp; But this notification not written to file, and was lost when power was cycled.&nbsp; Thus, we thought we were onto cartridge #2, but in reality were on #1 (which started working....).&nbsp; Sampling was as follows:

&nbsp;All cartridges started filtering at 60m depth while vehicle ascended to surface, where filtering stopped.&nbsp; WF took CTD casts in the same area at same time.&nbsp; Kevan took 2L each from each of these bottles: 60m, 40m, 20m, 10m, surface and mixed the 10L in a carboy.&nbsp; From that carboy, he sampled 1L through a cartridge on tackle-box, and 1L (x3) on peristaltic.&nbsp; Sample #2 had 1L (x3) through the tacklebox cartridge.&nbsp; Francisco took 1L from each of those depths and peristaltic filtered.

&nbsp;Because of the cartridge number mix-up, Honu returned with a dry #5 cartridge, which we ran as a negative control in the lab.&nbsp; Investigation of the alignment issues is ongoing.
\\

h3. Summary of 3G flights to this point (May 2017):

{panel}
*Nov* {color:#0000ff}2014{color} &nbsp;
Very first 3G flight.&nbsp; Makai with one Archive cartridge.&nbsp; Mission lasted \~3 days.
\_____________________\_
*July* {color:#0000ff}2015{color} &nbsp;
First 5-cartridge flight on Makai.&nbsp; All Archive.&nbsp; Cartridge 1 toroid valve stuck in bypass mode, thus recovered only 4 sample filters.&nbsp; All collected <20m deep.

*Dec* {color:#0000ff}2015{color} &nbsp;
First 4 & 1 (archive/LnG) flight on Makai.&nbsp; Many vehicle errors.&nbsp; No stratification so difficult to find any 'features'.&nbsp; Acquired 2 archives and 1 LnG.&nbsp; rough weather recovery.&nbsp; I don't have actual collection depths for these three samples.
\_____________________\_
*Feb* {color:#0000ff}2016{color} &nbsp;
Repeat Dec flight.&nbsp; 1 LnG fired first, then 4 Archives on Makai.&nbsp; Samples taken at 8.7m, 12.7m, 13m, 27m, and 27m.

*Dec* {color:#0000ff}2016{color} &nbsp;
Depth testing with Honu in Makai.&nbsp; 5 archival cartridges.&nbsp; Fired at chl max (~14m), 50m, and 100m.&nbsp; 200m cartridge started, but vehicle cut ESP power before finished.&nbsp; 300m sample had carousel alignment issue and did not complete.&nbsp; 3 of 5 samples preserved.
\_____________________\_
*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; meet with R/V Shimada (CALCOFI ship).&nbsp; Difficulties with water in payload section and rough recovery.&nbsp; Three filters recovered (chl-max to compare to Shimada's, and two at 10m)

*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; CANON cruise and WF rendezvous.&nbsp; Alignment problem had us bypass (so we thought) cartridge #1.&nbsp; Four archives collected, two a smear from 40m to surface, two from 60m to surface.&nbsp; These are matched to ship samples Kevan collected.
\_____________________\_

Overall, we have 21 archival filters that correctly filtered and preserved samples; two LnG samples were collected (were both run through SPR on the vehicle?)
{panel}

h3.]]></property>
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# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]
# [04Sep2008]
# [11Sep2008]
# [18Sep2008]
# [25Sep2008]
# [02Oct2008] (Pre-deployment discussions)
# [09Oct2008] (the day after deployment....)]]></property>
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<property name="body"><![CDATA[h5. {color:#3300ff}Thanks to the entire team for making yesterday's deployment...{color}


h5.


h3. Deployment Update

ESP Mack (SC)-\- radio-link weaker than expected.&nbsp; Brent going to do some home tweaking to see if he can get better signal

ESP Bruce (M0)-\- new CTD is not playing well with driver code.&nbsp; Possible solution has been pushed to it. Bob H. and Brent working on other solutions.&nbsp; Gaps in CTD data have no effect on ESP core runs.

ESP NEO (M0)--Linus kernel has frozen for a second time.&nbsp; It seems to take an exception, writes a log of it, try again, log again, and builds 30MB log file.&nbsp; Brent finally got in and restarted Linux.&nbsp; We used 3 pucks; 4 remaining BAC arrays are next up. This may be due to an updated SLP protocol with our old kernel...

&nbsp;Monitoring during this deployment

Chris S. and Brent will get all bad news; Chris email, Brent email and phone text.&nbsp; Cheri will receive bad news text messages as backup.

Chris P. will receive all messages via email, with the chore of looking for procedures that do not occur (not necessarily bad news).\\

Pickup date is Monday, Oct 27 with Shanna Rae.&nbsp; Will drive to SC, got get 'em, return to Moss landing.


h3. Machine Builds

* Dwarf Boards:
** boards that failed inspection (~30%) will&nbsp; be resoldered when Dick returns from vacation (Oct 20), and retested.
** Wayne writing a 'theory of operation' for dwarf and R-valve boards and will meet with Brent to get an overview, and bounce ideas.
* Cheri: will provide a build schedule for Moe. This needed so we can plan the McLane visit(s) during the build of the next two cores.
* By the end of next week, Addie will have a total parts order for ALL remaining MFB's.&nbsp; We'll submit to a shop in San Jose as El Camino is too busy.&nbsp; This will allow a visit from Mclane for MFB construction in early December.
* USB Camera: new camera's are not backward (slower speed) compatible w/ our boards
** We have a 2-stage decision:&nbsp;
*** talk to company about fixing their camera firmware to be truly backward compatible-Brent will try to get to them next week.
*** put something b/w the camera and our board that will allow USB 2.0 to work with our slower boards.&nbsp; These are commercially available.

h3. MFB


h3. Software


h3. DWSM

* Tapemation machinist on vacation.&nbsp; No sphere work performed since last week&nbsp;&nbsp;&nbsp;
* Ray having difficulties with swiss cheese plate: our CNC not quite beefy enough; he and Doug working on a solution
h6.

h3. GUI Development


h3. Other Items:]]></property>
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<property name="body"><![CDATA[Jim and Chris will be gone next 2-3 weeks.&nbsp;

h2. Plans to be completed by week of June 30:


h3. Tech Transfer

* Finish NEO temperature calibration then give to Science for exercising
* verify boards for MOE and mount/install
* start fluidic buildup
* waiting on several items (pressure sensor, various machining from El Camino)&nbsp;

h3. MFB

* Finishing SCWRRP samples this week
* Yesterday laid out detailed decision-tree on future experiments
* Chris P. to make sure enough MM, P/P, template for uninterrupted runs for next 3 weeks
* Tony fed-ex'd PCR tubing yesterday.&nbsp; Arrived today.
* SPE heater elements had to be sent back to company for thermal-conductive adhesive, which they forgot to apply.

h3. Software

* Communications w/ Bruce are intermittent.&nbsp; Should check buoy for kelp and/or position
* Mack showing large dB loss in its communication.&nbsp; Brent suggests we take off some of coiled cable in roof antenna to give us a few dB more signal.
* Brent to work with Roman to re-structure ESPshare for better file arrangement.
* A newer version of the 'notifier' software will queue both good and bad news and hold in queue until sent.

h3. DWSM

* Doug will finish bell housing designs, have them reviewed internally, and send to El Camino for quote
* Finish designs of mag coupling pressure shrouds.&nbsp; We will manufacture here
* Finish design on swiss cheese plates
* order valves
* high-pressure motor should arrive next week

h3. Other Items

* &nbsp;Chris S. has noticed that during this network deployment, images on Bruce consistently coming in dimmer than Mack, even though both have identical reagents.&nbsp; We believe images were the same before deployment.&nbsp; Scott thinks it could be due to differences in camera electronics due to the cold.
* CDR continuation:&nbsp; DWSM electronics and software CDR will be {color:#ff0000}{*}Weds. July 9{*}{color}.&nbsp; Invitations will be sent to Tom O., Mike Risi, Kevin G. Doug Au, Ed M., Chad K., Paul Mcgill.
* Scott still needs to do preliminary design of ROV mate-able interface and pressure board so plenty of work before CDR.
* Bruce/MACK recover is Monday, June 30.

h3.



Congratulations to everybody on a great deployment.&nbsp; We have three working instruments, two in the water for over 2 weeks, and much science data to chew on from this successful engineering effort.]]></property>
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<property name="body"><![CDATA[Jim and Chris will be gone next 2-3 weeks.&nbsp; Plans to be completed by week of June 30:

h3. Tech Transfer

* Finish NEO temperature calibration then give to Science for exercising
* verify boards for MOE and mount/install
* start fluidic buildup
* waiting on several items (pressure sensor, various machining from El Camino)&nbsp;

h3. MFB

* Finishing SCWRRP samples this week
* Yesterday laid out detailed decision-tree on future experiments
* Chris P. to make sure enough MM, P/P, template for uninterrupted runs for next 3 weeks
* Tony fed-ex'd PCR tubing yesterday.&nbsp; Should be here today or tomorrow.

h3. Software

* Communications w/ Bruce are intermittent.&nbsp; Should check buoy for kelp and/or position
* Mack showing large dB loss.&nbsp; Brent suggests we take off some of coiled cable in roof antenna to give us a few dB more signal.
* Brent to work with Roman to re-structure ESPshare for better file arrangement.
* A newer version of the 'notifier' software will queue both good and bad news and hold in queue until sent.
* Chris has notices that during this network deployment, images on Bruce consistently coming in dimmer than Mack even with identical reagents.&nbsp; We believe images were the same before deployment.&nbsp; Scott thinks it could be due to differences in camera electronics due to the cold.

h3. DWSM

* Doug will finish bell housing designs, have them reviewed internally, and send to El Camino for quote
* Finish designs of mag coupling pressure shrouds.&nbsp; We will manufacture here
* Finish design on swiss cheese plates
* order valves

h3. Other Items

* &nbsp;]]></property>
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<property name="body"><![CDATA[{mockup:testmock|2}

h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 17 July 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2017Jul08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Birch, Everlove, Jensen, Pargett, Harris, Roman, Gomes
Absent: Scholin

h3. Tech Transfer

* Cheri has started putting orders in for CMORE core we're building

* MACK doing first post-rebagging runs.  QCing reagents today.  If good, we'll load with pucks

* BRUCE: will start today with qualifying assay runs.  Going in cold {color:#ff0000}MAY 5{color}.  Will use GG's lid.

* NEO: has all new valves. Positioning needs verification.
* hand needs finishing, swapping, and calibration
* Neo goes in cold room {color:#cc0000}MAY 12{color}.  Will use new lid.

h3. Deployment

* Bail is being modified with weld so divers don't need to strap it on launch/recovery
* ISUS needs refurbishing-has been left with Luke who will do it early next week
* Monday Scott to work with Jose to refurbish battery pack (will be using a new one); for the 19 day deployemnt we used \~1/2 the battery pack.  Probably get 6 weeks from full pack.
* Mike notified about diver needs
* Zephyr on Thursday @ 7am, leave @ 8am.

h3. MFB

* New block from LLNL arrived this week.  Several scripting changes have been implemented which have helped stop killing our probe label.  We have run slugs on old and new blocks, and gotten very nice endpoint results.  Gels still to be run.

* Backgrounds on the two optical channels still are high (with water, 1630-1700 depending on channel).

* Need to find new heater vendor; Addie working on this

* Solid Phase extraction columns.  Order approved, but building it becoming a problem.  Addie trying to track down our original manufacturer.

* Must check with Mike Parker to see how his tombstone design on Moe is coming along.

h3. Software

* NEO -- firmware and Linux host needs updating
* MACK -- needs Ruby with email notification.  Brent will change and then exercise it through some mini-missions

h3. Sphere and 4K DWSMS

*Must pull together a deployment plan for the Lobos and DWSM as there are still big holes in the DWSM plan.
* Mtg scheduled for April 30.
* Scott has gotten one of the brushed motors to work off the dwarf (GOOD NEWS) so we can drive high power things directly from dwarfs.  Discussion to these benefits/logistics to be taken offline.

h3. GUI Development

* The deployment GUI has been used for two deployments, and Kevin continues to get feedback and tweak it with each subsequent deployment.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Birch, Everlove, Jensen, Pargett, Harris, Roman, Gomes
Absent: Scholin

h3. Tech Transfer

* Cheri has started putting orders in for CMORE core we're building

* MACK doing first post-rebagging runs.  QCing reagents today.  If good, we'll load with pucks

* BRUCE: will start today with qualifying assay runs.  Going in cold {color:#ff0000}MAY 5{color}.  Will use GG's lid.

* NEO: has all new valves. Positioning needs verification.
**hand needs finishing, swapping, and calibration
**Neo goes in cold room MAY 12.  Will use new lid.

h3. MFB

* New block from LLNL arrived this week.  Several scripting changes have been implemented which have helped stop killing our probe label.  We have run slugs on old and new blocks, and gotten very nice endpoint results.  Gels still to be run.

*Backgrounds on the two optical channels still are high (with water, 1630-1700 depending on channel).

*Need to find new heater vendor; Addie working on this

*Solid Phase extraction columns.  Order approved, but building it becoming a problem.  Addie trying to track down our original manufacturer.

*Must check with Mike Parker to see how his tombstone design on Moe is coming along.

h3. Software

Brent has a variety of software issues to work on, but most effort is focused on keeping Mack running smoothly

h3. Sphere and 4K DWSMS

Pumps continue to arrive.&nbsp; Two additional surface cans have various manufacturing defects.&nbsp; Doug working with Mike Parker to determine which pieces get sent back.

h3. GUI Development

Not discussed

Deployment issues discussed.&nbsp; We have asked and been granted permission to stage ESP in Bldg D.&nbsp; Discussion ensued about our reputation before and after deployments, and whether we should have a dedicated support person to help pre and post-deployment activities proceed smoothly.&nbsp; We will ask Mark B. if Jim Scholfield might be that person.&nbsp; Must check with Chris S. about having resources to use him.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Birch, Everlove, Jensen, Pargett, Harris, Roman, Gomes
Absent: Scholin

h3. Tech Transfer

* Cheri has started putting orders in for CMORE core we're building

* MACK doing first post-rebagging runs.  QCing reagents today.  If good, we'll load with pucks

* BRUCE: will start today with qualifying assay runs.  Going in cold {color:#ff0000}MAY 5{color}.  Will use GG's lid.

h3. MFB

\*New block from LLNL arrived this week.  Several scripting changes have been implemented which have helped stop killing our probe label.  We have run slugs on old and new blocks, and gotten very nice endpoint results.  Gels still to be run.

\*Backgrounds on the two optical channels still are high (with water, 1630-1700 depending on channel).

\*Need to find new heater vendor; Addie working on this

\*Solid Phase extraction columns.  Order approved, but building it becoming a problem.  Addie trying to track down our original manufacturer.

\*Must check with Mike Parker to see how his tombstone design on Moe is coming along.

h3. Software

Brent has a variety of software issues to work on, but most effort is focused on keeping Mack running smoothly

h3. Sphere and 4K DWSMS

Pumps continue to arrive.&nbsp; Two additional surface cans have various manufacturing defects.&nbsp; Doug working with Mike Parker to determine which pieces get sent back.

h3. GUI Development

Not discussed

Deployment issues discussed.&nbsp; We have asked and been granted permission to stage ESP in Bldg D.&nbsp; Discussion ensued about our reputation before and after deployments, and whether we should have a dedicated support person to help pre and post-deployment activities proceed smoothly.&nbsp; We will ask Mark B. if Jim Scholfield might be that person.&nbsp; Must check with Chris S. about having resources to use him.]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]
# [04Sep2008]
# [11Sep2008]
# [18Sep2008]
# [25Sep2008]]]></property>
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<property name="body"><![CDATA[Our first 'labeled' scintered frits arrived 23 April, 2008.&nbsp; These were 10um frits, labeled 'D'.
\\

The convention, decided in emails Feb 26, 2008, will be:

0.1, 0.5, 1, 10um frits will be labeled

A, B, C, D respectively.&nbsp;
\\

We have had CE Metallurgical make the 'press' for these so subsequent batches should be less expensive.&nbsp;
\\

Contact:

Chand Eisenmann Metallurgical
258 Spielman Hwy
Burlington, CT&nbsp; 06013

860-675-5000

email:
me@chandeisenmann.com&nbsp; (Mark)]]></property>
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<property name="body"><![CDATA[{mockup:testmock|2}

h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 17 July 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2017Jul08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]
# [Container/Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[{mockup:testmock|2}

h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 17 July 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2017Jul08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[h3. Deployment Update

* Jim Crisman has moved up his available dates.&nbsp; Means we must MOB Tuesday (Oct 7) and deploy Weds (Oct 8).
** M0--Bruce with new CTD
** M0--Neo with old CTD and ISUS
** SC--Mack with old CTD and ISUS
* Will run room-temp big pahse (PCR w/ LAF Bac concurrently) this afternoon.&nbsp; This is the PCR + WCR phase; 20\+ hrs.
* Brent still working on&nbsp; PCR/BAC integration
* For the entire deployment, NEO is doing only PCR/WCR and BAC/WCR
* Discussed the schedule (27th would be + cold, 28th would be - cold, 29th would be + cold)
* Running in cold we will use it in box, w/ ISUS and old CTD.&nbsp;

h3. Machine Builds

* Doug assembled harmonic drive on lathe for 'perfect' alignment.&nbsp; Power comparison to be performed this afternoon.&nbsp; We may have to redesign this with 2-shafted harmonic drive which will necessitate a different motor mount for the elbow joint.
* Puck temperature sensor on Moe--need more of them.&nbsp; Jim Montgomery can do this.&nbsp; Mounts for these are old--we need the newer sliding mounts.
* Ball screws--NOOK only made rev. D, which, according to our drawings WAS too small for us, but these seem as tight as the rev. E.&nbsp; Unclear what drawings they have (they say they've always built to rev. D drawings), so we must be very explicit in future orders--put rev on PO and call them for verbal confirmation.
* Dwarf Boards:
** have tested 15 of 35
** curious:&nbsp; after hand is closed, we still have voltage to the gripper drive.&nbsp; Must look into this after deployment.
** Will be finished by end of next week.

h3. MFB

* Syringe has been losing it's encoder position and over-filling until it hits the hard stop and overcurrents.&nbsp; First time, it pulled black plunger end off.&nbsp; Syringe has now been replaced and recalibrated.
* Still don't know reason; maybe losing encoder counts (9-30: yes--bug in Xylinx upgrade software seems to cause it; have reverted to older version and problem is gone)&nbsp;

h3. Software

* New CTD's have different firmware.&nbsp; Nontrivial.
* CS syringe on NEO has been changed
* Bruce--got stuck last night.&nbsp; Anytime tried to move a syringe or valve it hangs.&nbsp; It waits for a thread that's already dead.
* Mack--PS and clamp got corrupted (overcurrent errors).&nbsp; Sent out a 'recover' and it fixed it.
* Can't seem to FTP into shore station from his house
* Radio tests worked well, but while one file is uploading, link is monopolized (we can't talk to the other machines)
* Will give radio's to Jose
* Home syringe has been renamed.
* Firmware code still not frozen until Brent fixes: 1.&nbsp; Recover from hang due to dead thread, 2. Link protocols fixed, 3. CTD changes made

h3. DWSM

* Sphere on lathe at Tapemation
* Bulk-heads (swiss cheese plates) awaiting their turn in our shop
* Doug has some parts to be made; will give to Larry or Jose

h3. GUI Development

* &nbsp;Kevin working with Chris Preston on the new 'killer' mission planning app
* data analysis software being worked up right now.

h3. Other Items:


h5. Container:

* We will PURCHASE a container, but defer to future.&nbsp; Container information is here

h5. Build Schedule:

* &nbsp;Doug unsure if we will be ready for deep ESP testing in first week of January.&nbsp; Issue is that they are setting Lobos days for 2009, and we are slated for 5 days; they want us to take&nbsp; 4 days in Q1 and Q2, and they'll through in the 5th somewhere.&nbsp; We need a schedule from Doug on how the D-ESP testing will proceed with the ship days.&nbsp; Original plan was to start with passing fluid through the sphere, working toward a WF deployment before the big Axial trip.&nbsp; Doug should get a WAG schedule by end of day.

h5.


&nbsp;]]></property>
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<property name="body"><![CDATA[h3. Deployment Update


h3. Machine Builds


h3. MFB


h3. Software

* Brent working on firmware today and will hand-off HEX files to Wayne

h3. DWSM

* there is one piece of pressure testing for DWSM that is $6K.&nbsp; Approval given to purchase.

h3. GUI Development

* &nbsp;

h3. Other Items:
\\]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB 2007-08 Timeline |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.7|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1_7%2010_03_2008.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram4-22-08.ppt]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.7|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1_7%2010_03_2008.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram4-22-08.ppt]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.7|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1_7%2010_03_2008.doc]
# [PCR Users Manual v1.0|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20PCR%20Module%20Users%20Manual%20V1.0.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram4-22-08.ppt]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<id name="id">6226491</id>
<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.7|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1_7%10_03_2008.doc]
# [PCR Users Manual v1.0|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20PCR%20Module%20Users%20Manual%20V1.0.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram4-22-08.ppt]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.4|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1_7%10_03_2008.doc]
# [PCR Users Manual v1.0|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20PCR%20Module%20Users%20Manual%20V1.0.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram4-22-08.ppt]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.4|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.4%2004_05_2008.doc]
# [PCR Users Manual v1.0|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20PCR%20Module%20Users%20Manual%20V1.0.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram4-22-08.ppt]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 17 July 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2017Jul08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[h5. {color:#3300ff}Thanks to Scott, Brent, Roman, and Cheri for the long hours last night bringing Neo and Mack back to life...{color}



h5.


h3. Deployment Update

* MOB Tuesday PM, depart 06:30.&nbsp; Crew will be Chris S., Roman, Scott, divers: Lonny & Mike.&nbsp; Crane operator Luis, with x-tra pay for childcare/OT.
* Will deploy one @ MO, travel to SC, then back to M0 (allows 1 hr b/w each dive for divers)
* In water will fire off full-phase.&nbsp; Then rest and start on 11th.
* Moorings:&nbsp; lots of little things still to do, but coming along nicely.
* h4. The Plan:
** Mack and Bruce will be canned tomorrow (Friday).&nbsp; Bruce will be moved to it's mooring in preparation for radio testing.
** Brent will radio test Mack Friday.
** Saturday, Chris P will load PCR reagents on Neo.&nbsp; Then start a 24hr run lat Sat, making sure to do a full MFB with BAC run.&nbsp; This will confirm all reagents are good.&nbsp; {color:#cc0000}At start of this run will note power on Watts-up meter so we can get a power usage estimate for a full run{color}.
** Neo gets canned Monday
** Dual radio testing for Neo/Bruce Monday.

h3. Machine Builds

* Dwarf Boards:
** Dick soon to go on 2 wk vacation
** All boards tested.&nbsp; 6 R-valves fail.&nbsp; Failures came on motor tests.&nbsp; Could be Xylinx solder joints.
** Wayne writing a 'theory of operation' for dwarf and R-valve boards
* Issues with cores:
** Mack: replaced a dwarf board yesterday when it was acting unreliable.&nbsp; First board to go bad in long while.
** NEO:&nbsp; Brent fixed jittery Sample syringe brought about by too slow a minimum speed for integrator to adjust to. This change may need to be carried to all cores.
**** Brent noticed hand could not extend all the way.&nbsp; May be a calibration/config issue; will work with Scott on this
**** Software:&nbsp; issue with getting emails outside our firewall; Brent chewing on a fix for this.
*** Chris wants to run short IPC and SAR 11 to see if column is working.&nbsp; After that, run some negatives to show it's clean.&nbsp; then fire off a full SHA.

h3. MFB

* Grill progress stalled until Mike gets freed up.&nbsp; Addie asked to put in formal requests for work to get into que.
* New MFB user's manual will be on Confluence Friday or Monday.
* New LLNL module not tested; waiting on SPE heater block from Mike

h3. Software

* New CTD's have different firmware.&nbsp; Nontrivial.
* CS syringe on NEO has been changed
* Bruce--got stuck last night.&nbsp; Anytime tried to move a syringe or valve it hangs.&nbsp; It waits for a thread that's already dead.
* Mack--PS and clamp got corrupted (overcurrent errors).&nbsp; Sent out a 'recover' and it fixed it.
* Can't seem to FTP into shore station from his house
* Radio tests worked well, but while one file is uploading, link is monopolized (we can't talk to the other machines)
* Will give radio's to Jose
* Home syringe has been renamed.
* Firmware code still not frozen until Brent fixes: 1.&nbsp; Recover from hang due to dead thread, 2. Link protocols fixed, 3. CTD changes made

h3. DWSM

* Sphere bottom (2nd casting) is finished w/ rough out; needs finish work and ports milled
* Sphere top (1st casting) won't make shape, but machining adjustments will make it acceptable (or we'll de-rate it)
* Should be finished in 2-4 weeks
* Bulk-heads (swiss cheese plates) are in the mill and being processed.
* Doug soon to deliver large PO for Pressure transfer barrier (accumulator) for $6K
* h6. Elevator ideas:
** will have roughly 6'x6'x8' size.&nbsp; Lobos crew thinks size will be fine
** Doug believes 4 leg will be more stable than 3
** Foam pack findings:
*** 40lb/ft^3 will be $16K; 28lb/ft^3 will be $20K; Glass spheres will be $10K but much risk
*** will go with 28lb/ft^3; they say \~January delivery.&nbsp; Buying in brick format so useful for others after ESP project ends.
** Much brainstorming about elevator design, working at angles, how to counteract uneven surfaces, etc.

h3. GUI Development

* &nbsp;Kevin working with Chris Preston on the new 'killer' mission planning app; Chris having trouble running on her home machine
* data management software should be finished tomorrow.

h3. Other Items:

* Doug provided a 2009 deployment breakdown.&nbsp; Chris, Jim, Doug will discuss off-line before approaching Grech about schedule.]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp;
\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp; <!--  /* Font Definitions */ @font-face 	{font-family:Times; 	panose-1:2 0 5 0 0 0 0 0 0 0; 	mso-font-charset:0; 	mso-generic-font-family:auto; 	mso-font-pitch:variable; 	mso-font-signature:3 0 0 0 1 0;} @font-face 	{font-family:"MS ??"; 	mso-font-charset:78; 	mso-generic-font-family:auto; 	mso-font-pitch:variable; 	mso-font-signature:1 134676480 16 0 131072 0;} @font-face 	{font-family:"Cambria Math"; 	panose-1:2 4 5 3 5 4 6 3 2 4; 	mso-font-charset:0; 	mso-generic-font-family:auto; 	mso-font-pitch:variable; 	mso-font-signature:3 0 0 0 1 0;}  /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal 	{mso-style-unhide:no; 	mso-style-qformat:yes; 	mso-style-parent:""; 	margin:0cm; 	margin-bottom:.0001pt; 	mso-pagination:widow-orphan; 	font-size:12.0pt; 	font-family:Times; 	mso-fareast-font-family:"MS ??"; 	mso-fareast-theme-font:minor-fareast; 	mso-bidi-font-family:"Times New Roman"; 	mso-bidi-theme-font:minor-bidi; 	mso-fareast-language:JA;} .MsoChpDefault 	{mso-style-type:export-only; 	mso-default-props:yes; 	font-family:Cambria; 	mso-ascii-font-family:Cambria; 	mso-ascii-theme-font:minor-latin; 	mso-fareast-font-family:"MS ??"; 	mso-fareast-theme-font:minor-fareast; 	mso-hansi-font-family:Cambria; 	mso-hansi-theme-font:minor-latin; 	mso-bidi-font-family:"Times New Roman"; 	mso-bidi-theme-font:minor-bidi; 	mso-fareast-language:JA;} @page WordSection1 	{size:612.0pt 792.0pt; 	margin:72.0pt 90.0pt 72.0pt 90.0pt; 	mso-header-margin:36.0pt; 	mso-footer-margin:36.0pt; 	mso-paper-source:0;} div.WordSection1 	{page:WordSection1;} -->32.93592 \-117.31748 which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send) ]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)
\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.


Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp;
\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;

{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send)
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes (no longer maintained--Sep 2012)

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments](MB)
# [2009 Deployments](MB, MARS, SC Wharf)
# [2010 Deployments] (MB, SoCAL, Methane Mound, Drifter, MARS, SC Pier)
# [2011 Deployments](MB, GoM, Axial, Drifter-HI, SC Pier)
# [2012 Deployments] (MB, New Zealand, SoCAL, Friday Harbor, GoM, Drifter)
# [2013 Deployments] (MB, SoCAL, MARS, Puget Sound)
# [2014 Deployments] (MB, San Diego, Catalina, SoCAL, 3G)
# [2015 Deployments] (MB, SCRIPPS, 3G)
# [2016 Deployments] (3G in MB twice, SCRIPPS, Moran)
# 2017 Deployments (3G, SCRIPPS...)
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes (no longer maintained--Sep 2012)

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments](MB)
# [2009 Deployments](MB, MARS, SC Wharf)
# [2010 Deployments] (MB, SoCAL, Methane Mound, Drifter, MARS, SC Pier)
# [2011 Deployments](MB, GoM, Axial, Drifter-HI, SC Pier)
# [2012 Deployments] (MB, New Zealand, SoCAL, Friday Harbor, GoM, Drifter)
# [2013 Deployments] (MB, SoCAL, MARS, Puget Sound)
# [2014 Deployments] (MB, San Diego, Catalina, SoCAL, 3G)
# [2015 Deployments] (MB, SCRIPPS, 3G)
# [2016 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15-18, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;

h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 27, 2017*

Deployed for a rendevouz with the Flyer
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15-18, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;

h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 27, 2017*

This was part of a 5-vehicle launch (Tethys, Daphne, Aku w/ ESP Honu, Ahi, Opah).&nbsp; Gabe Foreman arrived from UH to help with piloting.&nbsp; Adam Jones helped launch Aku and Opah.


Multiple simulation runs to test mission.

Then on Weds, May 3, tried first 'real' concurrent sampling.&nbsp; Cartridge 1 threw an alignment error--could not push on plunge valve.&nbsp; Moved to cartridge 2, which took sample with WF \~2pm. ]]></property>
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<property name="body"><![CDATA[Present: Doug P, Addie, Chris S, Cheri, Brent, Scott, Kevin G, Jim, Visitor-Jack Regan

h3. Tech Transfer

* Mack running well so far. One week down\!
* We will try and keep the late May dates for pickup and dual deployment. May 27 Pickup Mack, May 28 Deploy Bruce & Neo. As dates approach, we'll decide on two teams; one team to ready two instruments, one for Mack pickup.
* Bruce:
** Temperature calibration on Monday after a weekend cool-down
** middle of week do roman flush
** end of week science gets it
* &nbsp;Cheri brought in reps from slider manufacturer.&nbsp; They have a model in which the races do not drift, but some parts of plastic.&nbsp; Unknown how this will respond to vapor environment in can.&nbsp; They left one slider, will send another, and we will begin temp and EtOH testing.
* Scott has prices on ordering/populating/building more dwarf and sleepy boards.&nbsp; Prices are as follows:
** Core: each needs 5 dwarves, 1 sleepy.&nbsp; Cost $7K for all components and wiring harnesses
** MFB: each needs 2 dwarves.&nbsp; Cost $2K for all components and wiring.
** This is what we decided we needed:
*** Dwarf boards:
**** Moe&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 6
**** CMORE&nbsp;&nbsp; 6
**** MFB&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 14
**** DWSM&nbsp;&nbsp;&nbsp;&nbsp; 6
**** Spares&nbsp;&nbsp;&nbsp; 10
*** 4 Sleepy boards

h3. MFB

* AIV hole sizes.&nbsp; It has been decided that we will order 10 custom AIV's, each with four 1/4-20 ports and two 10-32 ports.&nbsp; Rotors with custom grooves will have the 'larger' grooves to accommodate the 1/4-20 hole sizes.&nbsp; Addie will add DWSM components to any order she needs to place.
* Addie has found that the encoders we've been ordering are no longer made.&nbsp; Another manufacturer need be found.&nbsp; Group thinks this will not be difficult.
* Other things to order for big build:
** SPE columns
** motor gearing
** motor coupler
* SPE heater still needs some design work.&nbsp; Then must do cold testing.

h3. Software

* Low power boards.&nbsp; Decided that low power, long-term deployments were not on the schedule for the next 1\+ years, so resources will be redirected to other areas (e.g., a robust core).&nbsp; Brent had suggestions on things we could continue to look into to lower our power draw (power down battery, slow the CPU, change our intake/out-take hardware).&nbsp;
* Cheri found bug in puck counting when there was an arm miscalibration.&nbsp; Fix to be tested on Bruce.
* Brent working on implementing on Bruce e-mail notification of problems
* Working on modification fo firmware for DWSM.

h3. Sphere and 4K DWSMS

* Surface cans from IMT Precision.&nbsp;
** Cans have been 'repaired' and will arrive next week
** Scott to order lid connectors
** Doug to order lid plugs for pressure testing
** we will test with He and test tank
** Although out of spec, we will take one set of top/bottom lids.&nbsp; These to be tested&nbsp; once plugs arrive next week.
** lids to be moved to tin shed for storage until ready for use
* Doug to hold new DWSM design review in 2-3 weeks.

h3. GUI Development

* Kevin to meet with Brent to discuss issues related to mission scripting. ]]></property>
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# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]]]></property>
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# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# 17Apr2008]]></property>
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<property name="body"><![CDATA[Distribution list as of 05 Apr 2010:
\\
\\
|| MFB || PCR Module # || on Core || who gets? || ||
| tombstone | 9 \\ | NEO \\ | MBARI | |
| MFB1 | 1 | Moe | MBARI | |
| MFB2 | 5 | Betty | MBARI | |
| MFB3 | 4 | Gordon | MBARI | |
| MFB4 | 7 \\ | | CMORE | |
| MFB5 | 8 | | U. of Ga \\ | |
| MFB6 | 10 \\ | | Stanford | bleach leak causes flakey connector? |
| MFB7 | | | Harvard/Girgius | |
| MFB8 | none | | Harban's | |
| MFB9 | 13 \\ | | Caltech/Orphan | |
| MFB10 | 11 | | SCCWRP | |
| {color:#3366ff}&nbsp;MFB11{color} | 12 | | MBARI | under construction \\ |
| | | | | |
| | Spare: | | | |
| | 14 | | | |
| | 3 | | was originally on Tombstone, but moved #7 there for M0 deployment \\ | |]]></property>
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<property name="body"><![CDATA[Present: Doug P, Addie, Chris S, Cheri, Brent, Scott, Kevin G, Jim, Visitor-Jack Regan

h3. Tech Transfer

* Mack running well so far.  One week down\!
* We will try and keep the late May dates for pickup and dual deployment.  May 27 Pickup Mack, May 28 Deploy Bruce & Neo.  As dates approach, we'll decide on two teams; one team to ready two instruments, one for Mack pickup.
* Bruce:
** Temperature calibration on Monday after a weekend cool-down
** middle of week do roman flush
** end of week science gets it
* &nbsp;Cheri brought in reps from slider manufacturer.&nbsp; They have a model in which the races do not drift, but some parts of plastic.&nbsp; Unknown how this will respond to vapor environment in can.&nbsp; They left one slider, will send another, and we will begin temp and EtOH testing.
* Scott has prices on ordering/populating/building more dwarf and sleepy boards.&nbsp; Prices are as follows:
** Core: each needs 5 dwarves, 1 sleepy.&nbsp; Cost $7K for all components and wiring harnesses
** MFB: each needs 2 dwarves.&nbsp; Cost $2K for all components and wiring.
** This is what we decided we needed:
*** Dwarf boards:
**** Moe-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 6
**** CMORE-&nbsp;&nbsp; 6
**** MFB-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 14
**** DWSM-&nbsp;&nbsp;&nbsp;&nbsp; 6
**** Spares&nbsp;&nbsp;&nbsp;&nbsp; 10
*** 4 Sleepy boards

h3. MFB

* AIV hole sizes; what should we order?

h3. Software

* Low power boards.&nbsp; Decided that low power, long-term deployments were not on the schedule for the next 1\+ years, so resources will be redirected to other areas (e.g., a robust core).&nbsp; Brent had suggestions on things we could continue to look into to lower our power draw (power down battery, slow the CPU, change our intake/out-take hardware). &nbsp;

h3. Sphere and 4K DWSMS


h3. GUI Development]]></property>
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<property name="body"><![CDATA[Present: Doug P, Addie, Chris S, Cheri, Brent, Scott, Kevin G, Jim, Visitor-Jack Regan

h3. Tech Transfer

* Mack running well so far.  One week down!
* We will try and keep the late May dates for pickup and dual deployment.  May 27 Pickup Mack, May 28 Deploy Bruce & Neo.  As dates approach, we'll decide on two teams; one team to ready two instruments, one for Mack pickup.

h3. MFB

* AIV hole sizes; what should we order?

h3. Software

* Low power boards.&nbsp; When needed?&nbsp;

h3. Sphere and 4K DWSMS


h3. GUI Development]]></property>
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<property name="body"><![CDATA[h2. For discussion:


h3. Tech Transfer

* Bruce update

h3. MFB

* AIV hole sizes; what should we order?

h3. Software

* Low power boards.&nbsp; When needed?&nbsp;

h3. Sphere and 4K DWSMS


h3. GUI Development]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15-18, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;

h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 27\- May 8, 2017*

This was part of a 5-vehicle launch (Tethys, Daphne, Aku w/ ESP Honu, Ahi, Opah).&nbsp; Gabe Foreman arrived from UH to help with piloting.&nbsp; Adam Jones helped launch Aku and Opah.

Ran multiple simulation to test the mission.

On Weds, May 3, tried first 'real' concurrent sampling.&nbsp; Cartridge 1 threw an alignment error--could not push on plunge valve.&nbsp; We labeled that cartridge 'wet' and moved to cartridge 2.&nbsp; But this notification not written to file, and was lost when power was cycled.&nbsp; Thus, we thought we were onto cartridge #2, but in reality were on #1 (which started working....).&nbsp; Sampling was as follows:

&nbsp;All cartridges started filtering at 60m depth while vehicle ascended to surface, where filtering stopped.&nbsp; WF took CTD casts in the same area at same time.&nbsp; Kevan took 2L each from each of these bottles: 60m, 40m, 20m, 10m, surface and mixed the 10L in a carboy.&nbsp; From that carboy, he sampled 1L through a cartridge on tackle-box, and 1L (x3) on peristaltic.&nbsp; Sample #2 had 1L (x3) through the tacklebox cartridge.&nbsp; Francisco took 1L from each of those depths and peristaltic filtered.

&nbsp;Because of the cartridge number mix-up, Honu returned with a dry #5 cartridge, which we ran as a negative control in the lab.&nbsp; Investigation of the alignment issues is ongoing.\\

h3. Summarization of 3G flights to this point:


*Nov* 2014 &nbsp;
Very first 3G flight.&nbsp; Makai with one Archive cartridge.&nbsp; Mission lasted \~3 days.
\_____________________\_
*July* 2015 &nbsp;
First 5-cartridge flight on Makai.&nbsp; All Archive.&nbsp; Cartridge 1 toroid valve stuck in bypass mode, thus recovered only 4 sample filters.&nbsp; All collected <20m deep.

*Dec* 2015
First 4 & 1 (archive/LnG) flight on Makai.&nbsp; Many vehicle errors.&nbsp; No stratification so difficult to find any 'features'.&nbsp; Acquired 2 archives and 1 LnG.&nbsp; rough weather recovery.&nbsp; I don't have actual collection depths for these three samples.
\_____________________\_
*Feb* 2016
Repeat Dec flight.&nbsp; 1 LnG fired first, then 4 Archives on Makai.&nbsp; Samples taken at 8.7m, 12.7m, 13m, 27m, and 27m.

*Dec* 2016
Depth testing with Honu in Makai.&nbsp; 5 archival cartridges.&nbsp; Fired at chl max (~14m), 50m, and 100m.&nbsp; 200m cartridge started, but vehicle cut ESP power before finished.&nbsp; 300m sample had carousel alignment issue and did not complete.&nbsp; 3 of 5 samples preserved.
\_____________________\_
*Apr* 2017
5-archival mission. Honu on Aku; meet with R/V Shimada (CALCOFI ship).&nbsp; Difficulties with water in payload section and rough recovery.&nbsp; Three filters recovered (chl-max to compare to Shimada's, and two at 10m)

*Apr* 2017
5-archival mission. Honu on Aku; CANON cruise and WF rendezvous.&nbsp; Alignment problem had us bypass (so we thought) cartridge #1.&nbsp; Four archives collected, two a smear from 40m to surface, two from 60m to surface.&nbsp; These are matched to ship samples Kevan collected.
\_____________________\_

Overall, we have 21 archival filters that correctly filtered and preserved samples; two LnG samples were collected (were both run through SPR on the vehicle?)

h3. End Summary]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15-18, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;

h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 27\- May 8, 2017*

This was part of a 5-vehicle launch (Tethys, Daphne, Aku w/ ESP Honu, Ahi, Opah).&nbsp; Gabe Foreman arrived from UH to help with piloting.&nbsp; Adam Jones helped launch Aku and Opah.

Ran multiple simulation to test the mission.

On Weds, May 3, tried first 'real' concurrent sampling.&nbsp; Cartridge 1 threw an alignment error--could not push on plunge valve.&nbsp; We labeled that cartridge 'wet' and moved to cartridge 2.&nbsp; But this notification not written to file, and was lost when power was cycled.&nbsp; Thus, we thought we were onto cartridge #2, but in reality were on #1 (which started working....).&nbsp; Sampling was as follows:

&nbsp;All cartridges started filtering at 60m depth while vehicle ascended to surface, where filtering stopped.&nbsp; WF took CTD casts in the same area at same time.&nbsp; Kevan took 2L each from each of these bottles: 60m, 40m, 20m, 10m, surface and mixed the 10L in a carboy.&nbsp; From that carboy, he sampled 1L through a cartridge on tackle-box, and 1L (x3) on peristaltic.&nbsp; Sample #2 had 1L (x3) through the tacklebox cartridge.&nbsp; Francisco took 1L from each of those depths and peristaltic filtered.

&nbsp;Because of the cartridge number mix-up, Honu returned with a dry #5 cartridge, which we ran as a negative control in the lab.&nbsp; Investigation of the alignment issues is ongoing.
\\

h3. Summarization of 3G flights to this point:

{panel}
*Nov* {color:#0000ff}2014{color} &nbsp;
Very first 3G flight.&nbsp; Makai with one Archive cartridge.&nbsp; Mission lasted \~3 days.
\_____________________\_
*July* {color:#0000ff}2015{color} &nbsp;
First 5-cartridge flight on Makai.&nbsp; All Archive.&nbsp; Cartridge 1 toroid valve stuck in bypass mode, thus recovered only 4 sample filters.&nbsp; All collected <20m deep.

*Dec* {color:#0000ff}2015{color} &nbsp;
First 4 & 1 (archive/LnG) flight on Makai.&nbsp; Many vehicle errors.&nbsp; No stratification so difficult to find any 'features'.&nbsp; Acquired 2 archives and 1 LnG.&nbsp; rough weather recovery.&nbsp; I don't have actual collection depths for these three samples.
\_____________________\_
*Feb* {color:#0000ff}2016{color} &nbsp;
Repeat Dec flight.&nbsp; 1 LnG fired first, then 4 Archives on Makai.&nbsp; Samples taken at 8.7m, 12.7m, 13m, 27m, and 27m.

*Dec* {color:#0000ff}2016{color} &nbsp;
Depth testing with Honu in Makai.&nbsp; 5 archival cartridges.&nbsp; Fired at chl max (~14m), 50m, and 100m.&nbsp; 200m cartridge started, but vehicle cut ESP power before finished.&nbsp; 300m sample had carousel alignment issue and did not complete.&nbsp; 3 of 5 samples preserved.
\_____________________\_
*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; meet with R/V Shimada (CALCOFI ship).&nbsp; Difficulties with water in payload section and rough recovery.&nbsp; Three filters recovered (chl-max to compare to Shimada's, and two at 10m)

*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; CANON cruise and WF rendezvous.&nbsp; Alignment problem had us bypass (so we thought) cartridge #1.&nbsp; Four archives collected, two a smear from 40m to surface, two from 60m to surface.&nbsp; These are matched to ship samples Kevan collected.
\_____________________\_

Overall, we have 21 archival filters that correctly filtered and preserved samples; two LnG samples were collected (were both run through SPR on the vehicle?)
{panel}

h3.]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15-18, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;

h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 27\- May 8, 2017*

This was part of a 5-vehicle launch (Tethys, Daphne, Aku w/ ESP Honu, Ahi, Opah).&nbsp; Gabe Foreman arrived from UH to help with piloting.&nbsp; Adam Jones helped launch Aku and Opah.

Ran multiple simulation to test the mission.

On Weds, May 3, tried first 'real' concurrent sampling.&nbsp; Cartridge 1 threw an alignment error--could not push on plunge valve.&nbsp; We labeled that cartridge 'wet' and moved to cartridge 2.&nbsp; But this notification not written to file, and was lost when power was cycled.&nbsp; Thus, we thought we were onto cartridge #2, but in reality were on #1 (which started working....).&nbsp; Sampling was as follows:

&nbsp;All cartridges started filtering at 60m depth while vehicle ascended to surface, where filtering stopped.&nbsp; WF took CTD casts in the same area at same time.&nbsp; Kevan took 2L each from each of these bottles: 60m, 40m, 20m, 10m, surface and mixed the 10L in a carboy.&nbsp; From that carboy, he sampled 1L through a cartridge on tackle-box, and 1L (x3) on peristaltic.&nbsp; Sample #2 had 1L (x3) through the tacklebox cartridge.&nbsp; Francisco took 1L from each of those depths and peristaltic filtered.

&nbsp;Because of the cartridge number mix-up, Honu returned with a dry #5 cartridge, which we ran as a negative control in the lab.&nbsp; Investigation of the alignment issues is ongoing.
\\

h3. Summarization of 3G flights to this point:

{panel}
*Nov* 2014 &nbsp;
Very first 3G flight.&nbsp; Makai with one Archive cartridge.&nbsp; Mission lasted \~3 days.
\_____________________\_
*July* 2015 &nbsp;
First 5-cartridge flight on Makai.&nbsp; All Archive.&nbsp; Cartridge 1 toroid valve stuck in bypass mode, thus recovered only 4 sample filters.&nbsp; All collected <20m deep.

*Dec* 2015
First 4 & 1 (archive/LnG) flight on Makai.&nbsp; Many vehicle errors.&nbsp; No stratification so difficult to find any 'features'.&nbsp; Acquired 2 archives and 1 LnG.&nbsp; rough weather recovery.&nbsp; I don't have actual collection depths for these three samples.
\_____________________\_
*Feb* 2016
Repeat Dec flight.&nbsp; 1 LnG fired first, then 4 Archives on Makai.&nbsp; Samples taken at 8.7m, 12.7m, 13m, 27m, and 27m.

*Dec* 2016
Depth testing with Honu in Makai.&nbsp; 5 archival cartridges.&nbsp; Fired at chl max (~14m), 50m, and 100m.&nbsp; 200m cartridge started, but vehicle cut ESP power before finished.&nbsp; 300m sample had carousel alignment issue and did not complete.&nbsp; 3 of 5 samples preserved.
\_____________________\_
*Apr* 2017
5-archival mission. Honu on Aku; meet with R/V Shimada (CALCOFI ship).&nbsp; Difficulties with water in payload section and rough recovery.&nbsp; Three filters recovered (chl-max to compare to Shimada's, and two at 10m)

*Apr* 2017
5-archival mission. Honu on Aku; CANON cruise and WF rendezvous.&nbsp; Alignment problem had us bypass (so we thought) cartridge #1.&nbsp; Four archives collected, two a smear from 40m to surface, two from 60m to surface.&nbsp; These are matched to ship samples Kevan collected.
\_____________________\_

Overall, we have 21 archival filters that correctly filtered and preserved samples; two LnG samples were collected (were both run through SPR on the vehicle?)
{panel}

h3.]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15-18, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;

h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 27\- May 8, 2017*

This was part of a 5-vehicle launch (Tethys, Daphne, Aku w/ ESP Honu, Ahi, Opah).&nbsp; Gabe Foreman arrived from UH to help with piloting.&nbsp; Adam Jones helped launch Aku and Opah.

Ran multiple simulation to test the mission.

On Weds, May 3, tried first 'real' concurrent sampling.&nbsp; Cartridge 1 threw an alignment error--could not push on plunge valve.&nbsp; We labeled that cartridge 'wet' and moved to cartridge 2.&nbsp; But this notification not written to file, and was lost when power was cycled.&nbsp; Thus, we thought we were onto cartridge #2, but in reality were on #1 (which started working....).&nbsp; Sampling was as follows:

&nbsp;All cartridges started filtering at 60m depth while vehicle ascended to surface, where filtering stopped.&nbsp; WF took CTD casts in the same area at same time.&nbsp; Kevan took 2L each from each of these bottles: 60m, 40m, 20m, 10m, surface and mixed the 10L in a carboy.&nbsp; From that carboy, he sampled 1L through a cartridge on tackle-box, and 1L (x3) on peristaltic.&nbsp; Sample #2 had 1L (x3) through the tacklebox cartridge.&nbsp; Francisco took 1L from each of those depths and peristaltic filtered.

&nbsp;Because of the cartridge number mix-up, Honu returned with a dry #5 cartridge, which we ran as a negative control in the lab.&nbsp; Investigation of the alignment issues is ongoing.]]></property>
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<property name="body"><![CDATA[Material still being added (4-11-08; 6:00pm)...&nbsp;

Present: Doug P, Addie, Chris S, Cheri, Brent, Scott, Kevin G, Jim, Visitor-Jack Regan

h3. Tech Transfer

* Mack running well so far.  One week down\!
* We will try and keep the late May dates for pickup and dual deployment.  May 27 Pickup Mack, May 28 Deploy Bruce & Neo.  As dates approach, we'll decide on two teams; one team to ready two instruments, one for Mack pickup.
* Bruce:
** Temperature calibration on Monday after a weekend cool-down
** middle of week do roman flush
** end of week science gets it
* &nbsp;Cheri brought in reps from slider manufacturer.&nbsp; They have a model in which the races do not drift, but some parts of plastic.&nbsp; Unknown how this will respond to vapor environment in can.&nbsp; They left one slider, will send another, and we will begin temp and EtOH testing.
* Scott has prices on ordering/populating/building more dwarf and sleepy boards.&nbsp; Prices are as follows:
** Core: each needs 5 dwarves, 1 sleepy.&nbsp; Cost $7K for all components and wiring harnesses
** MFB: each needs 2 dwarves.&nbsp; Cost $2K for all components and wiring.
** This is what we decided we needed:
*** Dwarf boards:
**** Moe-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 6
**** CMORE-&nbsp;&nbsp; 6
**** MFB-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 14
**** DWSM-&nbsp;&nbsp;&nbsp;&nbsp; 6
**** Spares&nbsp;&nbsp;&nbsp;&nbsp; 10
*** 4 Sleepy boards

h3. MFB

* AIV hole sizes.&nbsp; It has been decided that we will order 10 custom AIV's with two 1/4-20 ports, four 10-32 ports (ADDIE IS THIS CORRECT?).&nbsp; Rotors with custom grooves will have the 'larger' grooves to accomodate the 1/4-20 hole sizes.&nbsp; Addie will add DWSM components to any order she needs to place.
* Addie has found that the encoders we've been ordering are no longer made.&nbsp; Another manufacturer need be found.&nbsp; Group thinks this will not be difficult.

h3. Software

* Low power boards.&nbsp; Decided that low power, long-term deployments were not on the schedule for the next 1\+ years, so resources will be redirected to other areas (e.g., a robust core).&nbsp; Brent had suggestions on things we could continue to look into to lower our power draw (power down battery, slow the CPU, change our intake/out-take hardware). &nbsp;

h3. Sphere and 4K DWSMS


h3. GUI Development]]></property>
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<property name="body"><![CDATA[Present: Doug P, Addie, Chris S, Cheri, Brent, Scott, Kevin G, Jim, Visitor-Jack Regan

h3. Tech Transfer

* Mack running well so far.  One week down\!
* We will try and keep the late May dates for pickup and dual deployment.  May 27 Pickup Mack, May 28 Deploy Bruce & Neo.  As dates approach, we'll decide on two teams; one team to ready two instruments, one for Mack pickup.
* Bruce:
** Temperature calibration on Monday after a weekend cool-down
** middle of week do roman flush
** end of week science gets it
* &nbsp;Cheri brought in reps from slider manufacturer.&nbsp; They have a model in which the races do not drift, but some parts of plastic.&nbsp; Unknown how this will respond to vapor environment in can.&nbsp; They left one slider, will send another, and we will begin temp and EtOH testing.
* Scott has prices on ordering/populating/building more dwarf and sleepy boards.&nbsp; Prices are as follows:
** Core: each needs 5 dwarves, 1 sleepy.&nbsp; Cost $7K for all components and wiring harnesses
** MFB: each needs 2 dwarves.&nbsp; Cost $2K for all components and wiring.
** This is what we decided we needed:
*** Dwarf boards:
**** Moe-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 6
**** CMORE-&nbsp;&nbsp; 6
**** MFB-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 14
**** DWSM-&nbsp;&nbsp;&nbsp;&nbsp; 6
**** Spares&nbsp;&nbsp;&nbsp;&nbsp; 10
*** 4 Sleepy boards

h3. MFB

* AIV hole sizes.&nbsp; It has been decided that we will order 10 custom AIV's with two 1/4-20 ports, four 10-32 ports (ADDIE IS THIS CORRECT?).&nbsp; Rotors with custom grooves will have the 'larger' grooves to accomodate the 1/4-20 hole sizes.&nbsp; Addie will add DWSM components to any order she needs to place.
* Addie has found that the encoders we've been ordering are no longer made.&nbsp; Another manufacturer need be found.&nbsp; Group thinks this will not be difficult.

h3. Software

* Low power boards.&nbsp; Decided that low power, long-term deployments were not on the schedule for the next 1\+ years, so resources will be redirected to other areas (e.g., a robust core).&nbsp; Brent had suggestions on things we could continue to look into to lower our power draw (power down battery, slow the CPU, change our intake/out-take hardware). &nbsp;

h3. Sphere and 4K DWSMS


h3. GUI Development]]></property>
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<property name="body"><![CDATA[Present: Doug P, Addie, Chris S, Cheri, Brent, Scott, Kevin G, Jim, Visitor-Jack Regan

h3. Tech Transfer

* Mack running well so far.  One week down\!
* We will try and keep the late May dates for pickup and dual deployment.  May 27 Pickup Mack, May 28 Deploy Bruce & Neo.  As dates approach, we'll decide on two teams; one team to ready two instruments, one for Mack pickup.
* Bruce:
** Temperature calibration on Monday after a weekend cool-down
** middle of week do roman flush
** end of week science gets it
* &nbsp;Cheri brought in reps from slider manufacturer.&nbsp; They have a model in which the races do not drift, but some parts of plastic.&nbsp; Unknown how this will respond to vapor environment in can.&nbsp; They left one slider, will send another, and we will begin temp and EtOH testing.
* Scott has prices on ordering/populating/building more dwarf and sleepy boards.&nbsp; Prices are as follows:
** Core: each needs 5 dwarves, 1 sleepy.&nbsp; Cost $7K for all components and wiring harnesses
** MFB: each needs 2 dwarves.&nbsp; Cost $2K for all components and wiring.
** This is what we decided we needed:
*** Dwarf boards:
**** Moe&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 6
**** CMORE&nbsp;&nbsp; 6
**** MFB&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 14
**** DWSM&nbsp;&nbsp;&nbsp;&nbsp; 6
**** Spares&nbsp;&nbsp;&nbsp; 10
*** 4 Sleepy boards

h3. MFB

* AIV hole sizes.&nbsp; It has been decided that we will order 10 custom AIV's with two 1/4-20 ports, four 10-32 ports (ADDIE IS THIS CORRECT?).&nbsp; Rotors with custom grooves will have the 'larger' grooves to accomodate the 1/4-20 hole sizes.&nbsp; Addie will add DWSM components to any order she needs to place.
* Addie has found that the encoders we've been ordering are no longer made.&nbsp; Another manufacturer need be found.&nbsp; Group thinks this will not be difficult.
* Other things to order for big build:
** SPE columns
** motor gearing
** motor coupler
* SPE heater still needs some design work.&nbsp; Then must do cold testing.

h3. Software

* Low power boards.&nbsp; Decided that low power, long-term deployments were not on the schedule for the next 1\+ years, so resources will be redirected to other areas (e.g., a robust core).&nbsp; Brent had suggestions on things we could continue to look into to lower our power draw (power down battery, slow the CPU, change our intake/out-take hardware).&nbsp;
* Cheri found bug in puck counting when there was an arm miscalibration.&nbsp; Fix to be tested on Bruce.
* Brent working on implementing on Bruce e-mail notification of problems
* Working on modification fo firmware for DWSM.


h3. Sphere and 4K DWSMS

* Surface cans from IMT Precision.&nbsp;
** Cans have been 'repaired' and will arrive next week
** Scott to order lid connectors
** Doug to order lid plugs for pressure testing
** we will test with He and test tank
** Although out of spec, we will take one set of top/bottom lids.&nbsp; These to be tested&nbsp; once plugs arrive next week.
** lids to be moved to tin shed for storage until ready for use
* Doug to hold new DWSM design review in 2-3 weeks.

h3. GUI Development

* Kevin to meet with Brent to discuss issues related to mission scripting.]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 15-18, 2017*

This was flight to coincide with the CALCOFI ship, the R/V Shimada.&nbsp; We were to take a sample at the chl-max near the ship while they did their CTD cast.&nbsp; These two filters would be compared.&nbsp; Multiple problems with LRAUV and ESP.&nbsp; LRAUV launched on Apr 14 without a wet-test of the mission.&nbsp; That afternoon vehicle sounded its water alarm (water in payload section).&nbsp; Brett braved weather and recovered that afternoon but considerable damage to vehicle.&nbsp; Stayed late that evening and repaired.

Next morning (Saturday, Apr 15) Scott, Kevan, Brett, Jim opened Honu.&nbsp; 5-10 ml of water present.&nbsp; Eventually discovered loose swagelok fittings upstream of the bulkhead valves.&nbsp; These tightened, and we raced to make the Shimada rendezvous.&nbsp; Met north of M1, and put vehicle in water.&nbsp; took \~2 hrs for mission to finally load and begin; Shimada had drifted 500m to our southwest when sampling took place.&nbsp; Multiple vehicle/instrument issues after that; poor communications to vehicle.&nbsp; Incorrect cartridge volumes used the protocol so syringes kept bottoming-out.&nbsp; Vehicle recovered Apr 18.&nbsp; Three filters recovered; chl-max, and two at 10m.&nbsp; (?)\\

h4. {color:#ff00cc}Del Mar w/ ESP Waldo{color}

*Apr 18, 2017*

Deployment for Jon Zehr.&nbsp; Employed M/V Merlin with Walt Crampton and Jared ?&nbsp; Divers from SCRIPPs with Rich Walsh.&nbsp; Van 4 with 5'x9' Uhaul w/ramp trailer.

Used ESP-Waldo sitting \~10m.&nbsp; Two battery cans and CTD.&nbsp; MELO worked sporadically for 2 days, then stopped.&nbsp; Last location said:&nbsp;
{panel}
32.93592 \-117.31748
{panel}
which places it north of the Del Mar buoy (see attached [map of prior year deployments|^plot_map_delmar_pos_20170414.pdf] from Uwe Send). &nbsp;

h4. {color:#ff00cc}AKU flight w ESP-Honu and 5 Archive Cartridges{color}

*Apr 27\- May 8, 2017*

This was part of a 5-vehicle launch (Tethys, Daphne, Aku w/ ESP Honu, Ahi, Opah).&nbsp; Gabe Foreman arrived from UH to help with piloting.&nbsp; Adam Jones helped launch Aku and Opah.

Ran multiple simulation to test the mission.

On Weds, May 3, tried first 'real' concurrent sampling.&nbsp; Cartridge 1 threw an alignment error--could not push on plunge valve.&nbsp; We labeled that cartridge 'wet' and moved to cartridge 2.&nbsp; But this notification not written to file, and was lost when power was cycled.&nbsp; Thus, we thought we were onto cartridge #2, but in reality were on #1 (which started working....).&nbsp; Sampling was as follows:

&nbsp;All cartridges started filtering at 60m depth while vehicle ascended to surface, where filtering stopped.&nbsp; WF took CTD casts in the same area at same time.&nbsp; Kevan took 2L each from each of these bottles: 60m, 40m, 20m, 10m, surface and mixed the 10L in a carboy.&nbsp; From that carboy, he sampled 1L through a cartridge on tackle-box, and 1L (x3) on peristaltic.&nbsp; Sample #2 had 1L (x3) through the tacklebox cartridge.&nbsp; Francisco took 1L from each of those depths and peristaltic filtered.

&nbsp;Because of the cartridge number mix-up, Honu returned with a dry #5 cartridge, which we ran as a negative control in the lab.&nbsp; Investigation of the alignment issues is ongoing.
\\

h3. Summary of 3G flights to this point:

{panel}
*Nov* {color:#0000ff}2014{color} &nbsp;
Very first 3G flight.&nbsp; Makai with one Archive cartridge.&nbsp; Mission lasted \~3 days.
\_____________________\_
*July* {color:#0000ff}2015{color} &nbsp;
First 5-cartridge flight on Makai.&nbsp; All Archive.&nbsp; Cartridge 1 toroid valve stuck in bypass mode, thus recovered only 4 sample filters.&nbsp; All collected <20m deep.

*Dec* {color:#0000ff}2015{color} &nbsp;
First 4 & 1 (archive/LnG) flight on Makai.&nbsp; Many vehicle errors.&nbsp; No stratification so difficult to find any 'features'.&nbsp; Acquired 2 archives and 1 LnG.&nbsp; rough weather recovery.&nbsp; I don't have actual collection depths for these three samples.
\_____________________\_
*Feb* {color:#0000ff}2016{color} &nbsp;
Repeat Dec flight.&nbsp; 1 LnG fired first, then 4 Archives on Makai.&nbsp; Samples taken at 8.7m, 12.7m, 13m, 27m, and 27m.

*Dec* {color:#0000ff}2016{color} &nbsp;
Depth testing with Honu in Makai.&nbsp; 5 archival cartridges.&nbsp; Fired at chl max (~14m), 50m, and 100m.&nbsp; 200m cartridge started, but vehicle cut ESP power before finished.&nbsp; 300m sample had carousel alignment issue and did not complete.&nbsp; 3 of 5 samples preserved.
\_____________________\_
*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; meet with R/V Shimada (CALCOFI ship).&nbsp; Difficulties with water in payload section and rough recovery.&nbsp; Three filters recovered (chl-max to compare to Shimada's, and two at 10m)

*Apr* {color:#0000ff}2017{color} &nbsp;
5-archival mission. Honu on Aku; CANON cruise and WF rendezvous.&nbsp; Alignment problem had us bypass (so we thought) cartridge #1.&nbsp; Four archives collected, two a smear from 40m to surface, two from 60m to surface.&nbsp; These are matched to ship samples Kevan collected.
\_____________________\_

Overall, we have 21 archival filters that correctly filtered and preserved samples; two LnG samples were collected (were both run through SPR on the vehicle?)
{panel}

h3.]]></property>
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<property name="body"><![CDATA[h4. (as of Mar 28, 2013)


h3. Surface Mooring Cables

35.5m (w/ floats) 35 day S. Cal ECOHAB w/ Bruce (Mar 2013)


25.5m (bare)

25.3m (bare)

21.5m (w/ floats)

15.6m (w/ floats) 35 day S. Cal ECOHAB w/Mack (Mar 2013)


15.2m (w/ floats)

h3. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them. ]]></property>
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<property name="body"><![CDATA[h4. (as of Mar 28, 2013)


h3. Surface Mooring Cables

35.5m (w/ floats)
* 35 day S. Cal ECOHAB w/ Bruce (Mar 2013)

25.5m (bare)

25.3m (bare)

21.5m (w/ floats)

15.6m (w/ floats)
* 35 day S. Cal ECOHAB w/Mack (Mar 2013)
* 41 day MB ECOHAB w/Mack (Sep 2013)

15.2m (w/ floats)
* 41 day MB ECOHAB w/Mack (Sep 2013)&nbsp;

h3. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them. ]]></property>
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<property name="body"><![CDATA[h4. (as of Mar 28, 2013)


h3. Surface Mooring Cables

35.5m (w/ floats) \--35 day S. Cal ECOHAB w/ Bruce (Mar 2013)
25.5m (bare)

25.3m (bare)

21.5m (w/ floats)

15.6m (w/ floats) \--35 day S. Cal ECOHAB w/Mack (Mar 2013)

\--41 day MB ECOHAB w/Mack (Sep 2013)

15.2m (w/ floats)\--41 day MB ECOHAB w/Mack (Sep 2013)&nbsp;

h3. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them. ]]></property>
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<property name="body"><![CDATA[h4. (as of Mar 28, 2013)


h3. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 day S. Cal ECOHAB w/ Bruce (Mar 2013)

*25.5m (bare)*

*25.3m (bare)*

*21.5m (w/ floats)*

*15.6m (w/ floats)*
* 35 day S. Cal ECOHAB w/Mack (Mar 2013)
* 41 day MB ECOHAB w/Mack (Sep 2013)

*15.2m (w/ floats)*
* 41 day MB ECOHAB w/Mack (Sep 2013)&nbsp;

h3. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them. ]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|ESPAPP:G3 IO list]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[Control Loops

|| || Control Loops \\ || Inputs \\ || Outputs ||
| | Sampling Pump\\ | | |
| | Spool Valve actuator\\ | | |
| | Cylinder Rotate\\ | | |
| | | | |
| | | | |
| | | | |
| | | | |
| | | | |
| | | | |
| | | | |
| | | | |
| | | | |
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\\]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 8 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-1.2.3.jar] to your computer.
# Double-click the jar to run the app.

You can also get the automated image analysis application [here|http://www.mbari.org/staff/brian/software/esp-automated-imaging-0.3.jar]

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|Investigations into Automated Image Analysis].

I'm working on a new method. Documentation is [here|ESP Automated Image Analysis 2]

h1. How to use it


h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls

!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.
{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size.
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result

!filter_3-20090430221134.png!

h3. Data Result

{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

h4. {color:#ff00cc}Puget Sound{color}

_{+}Lummi Bay:+_

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)

*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.&nbsp; Subsequent investigation found that modem card had been cancelled with T-Mobile due to NOAA miscommunication.&nbsp; When new one was tried, operator did not know to 'close the door' on the modem in order to power the card.&nbsp; Brent flew up and fixed.&nbsp; Missed 4 days of sampling.

*August 18*\--Lummi Bay deployment ended.&nbsp; Machine returned to NOAA.

_{+}Samish Bay:&nbsp;+_

*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; No CTD.&nbsp; Both machines have MFB and PCR.&nbsp; Media event was July 18.

Aug 14--Recover Gordon

Aug 17--Deploy (swap) NEO.

Sep 10--processing syringe servo motor has failed.&nbsp; Decision to run out remaining mission with archive only.

*Sep 16*\--NEO's mission ends.&nbsp; NOAA to recover and Roman/Kevan retrieved both machines Sep 25.

h4. {color:#ff00cc}ECOHAB/CANON--Monterey Bay{color}

*&nbsp;September 10, 2013*\-\- Deploy 2 ESP's in Monterey Bay.&nbsp; First time in southern part of bay.

'North'
ESP-Mack.&nbsp; Lat 36.9048, Long \-121.93659, Water depth 32m, Can depth 9.8m.
\\

'South'
ESP-Bruce. Lat 36.63908, Long \-121.87884, Water depth 60m, Can depth 4.8m

*Oct 10, 2013*\-\-Found 'terminal fluid retention' on processing side--pulled an oring or some type of leak. ]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

h4. {color:#ff00cc}Puget Sound{color}

_{+}Lummi Bay:+_

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)

*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.&nbsp; Subsequent investigation found that modem card had been cancelled with T-Mobile due to NOAA miscommunication.&nbsp; When new one was tried, operator did not know to 'close the door' on the modem in order to power the card.&nbsp; Brent flew up and fixed.&nbsp; Missed 4 days of sampling.

*August 18*\--Lummi Bay deployment ended.&nbsp; Machine returned to NOAA.

_{+}Samish Bay:&nbsp;+_

*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; No CTD.&nbsp; Both machines have MFB and PCR.&nbsp; Media event was July 18.

Aug 14--Recover Gordon

Aug 17--Deploy (swap) NEO.

Sep 10--processing syringe servo motor has failed.&nbsp; Decision to run out remaining mission with archive only.

*Sep 16*\--NEO's mission ends.&nbsp; NOAA to recover and Roman/Kevan retrieved both machines Sep 25.

h4. {color:#ff00cc}ECOHAB/CANON--Monterey Bay{color}

*&nbsp;September 10, 2013*\-\- Deploy 2 ESP's in Monterey Bay.&nbsp; First time in southern part of bay.

'North'
ESP-Mack.&nbsp; Lat 36.9048, Long \-121.93659, Water depth 32m, Can depth 9.8m.

*Oct 11, 2013*\--Battery voltage dropped too low, and we had to end mission


'South'
ESP-Bruce. Lat 36.63908, Long \-121.87884, Water depth 60m, Can depth 4.8m

*Oct 10, 2013*\--Found 'terminal fluid retention' on processing side--pulled an oring or some type of leak. ]]></property>
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<property name="body"><![CDATA[Instrument Level
|| || Control Loops&nbsp; || || Inputs \\ || Outputs || || || || || ||
| 1 \\ | Sampling Pump \\ | | | | | | | | |
| 2 | Spool Valve actuator \\ | | | | | | | | |
| 3 | Cylinder Rotate \\ | | | | | | | | |
| 4 | Cartridge Actuator Alignment \\ | | | | | | | | |
| 5 | Cartridge Actuator 1 \\ | | | | | | | | |
| 6 | Cartridge Actuator 2 | | | | | | | | |
| 7 | Cartridge Actuator 3 | | | | | | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | | | | | | |
| 9 | Cartridge Actuator Reagent Valve \\ | | | | | | | | |
| 10 | A/M Clamp \\ | | | | | | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | | | | | | |
| 12 | A/M Hand-off Syringe \\ | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
\\
|| ||  Discrete Actions || || \\ || Outputs || || || || || ||
| 1 \\ | Intake Select 1 \\ | | | | | | | | |
| 2 | Intake Select 2 \\ | | | | | | | | |
| 3 | Bulkhead valve (intake) \\ | | | | | | | | |
| 4 | Bulkhead valve (exhaust) | | | | | | | | |
| 5 | Cartridge Valve Actuator 1 \\ | | | | | | | | |
| 6 | Cylinder latch\\ | | | | | | | | |
| 7 | A/M Valve 1\\ | | | | | | | | |
| 8 | A/M Valve 2\\ | | | | | | | | |
| 9 | A/M Valve 3 | | | | | | | | |
| 10 | A/M Valve 4 | | | | | | | | |
| 11 | A/M Clamp \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
\\]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

h4. {color:#ff00cc}Puget Sound{color}

_{+}Lummi Bay:+_

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)

*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.&nbsp; Subsequent investigation found that modem card had been cancelled with T-Mobile due to NOAA miscommunication.&nbsp; When new one was tried, operator did not know to 'close the door' on the modem in order to power the card.&nbsp; Brent flew up and fixed.&nbsp; Missed 4 days of sampling.

*August 18*\--Lummi Bay deployment ended.&nbsp; Machine returned to NOAA.

_{+}Samish Bay:&nbsp;+_

*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; No CTD.&nbsp; Both machines have MFB and PCR.&nbsp; Media event was July 18.

Aug 14--Recover Gordon

Aug 17--Deploy (swap) NEO.

Sep 10--processing syringe servo motor has failed.&nbsp; Decision to run out remaining mission with archive only.

*Sep 16*\--NEO's mission ends.&nbsp; NOAA to recover and Roman/Kevan retrieved both machines Sep 25.

h4. {color:#ff00cc}ECOHAB/CANON--Monterey Bay{color}

*&nbsp;September 10, 2013*\-\- Deploy 2 ESP's in Monterey Bay.&nbsp; First time in southern part of bay.

{color:#cc3366}'North'{color}
ESP-Mack.&nbsp; Lat 36.9048, Long \-121.93659, Water depth 32m, Can depth 9.8m.

*Oct 11, 2013*\--Battery voltage dropped too low, and we had to end mission

{color:#cc3366}'South'{color}
ESP-Bruce. Lat 36.63908, Long \-121.87884, Water depth 60m, Can depth 4.8m

*Oct 10, 2013*\-Found 'terminal fluid retention' on processing side-pulled an oring or some type of leak. Tried porting waste to Waste2 (known to be empty), but same results.  Final 3 samples to try and collect for SEM work.]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

h4. {color:#ff00cc}Puget Sound{color}

_{+}Lummi Bay:+_

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)

*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.&nbsp; Subsequent investigation found that modem card had been cancelled with T-Mobile due to NOAA miscommunication.&nbsp; When new one was tried, operator did not know to 'close the door' on the modem in order to power the card.&nbsp; Brent flew up and fixed.&nbsp; Missed 4 days of sampling.

*August 18*\--Lummi Bay deployment ended.&nbsp; Machine returned to NOAA.

_{+}Samish Bay:&nbsp;+_

*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; No CTD.&nbsp; Both machines have MFB and PCR.&nbsp; Media event was July 18.

Aug 14--Recover Gordon

Aug 17--Deploy (swap) NEO.

Sep 10--processing syringe servo motor has failed.&nbsp; Decision to run out remaining mission with archive only.

*Sep 16*\--NEO's mission ends.&nbsp; NOAA to recover and Roman/Kevan retrieved both machines Sep 25.

h4. {color:#ff00cc}ECOHAB/CANON--Monterey Bay{color}

*&nbsp;September 10, 2013*\-\- Deploy 2 ESP's in Monterey Bay.&nbsp; First time in southern part of bay.

'North'
ESP-Mack.&nbsp; Lat 36.9048, Long \-121.93659, Water depth 32m, Can depth 9.8m.

*Oct 11, 2013*\--Battery voltage dropped too low, and we had to end mission

'South'
ESP-Bruce. Lat 36.63908, Long \-121.87884, Water depth 60m, Can depth 4.8m

*Oct 10, 2013*\--Found 'terminal fluid retention' on processing side--pulled an oring or some type of leak. Tried porting waste to Waste2 (known to be empty), but same results.  Final 3 samples to try and collect for SEM work.]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

h4. {color:#ff00cc}Puget Sound{color}

_{+}Lummi Bay:+_

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)

*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.&nbsp; Subsequent investigation found that modem card had been cancelled with T-Mobile due to NOAA miscommunication.&nbsp; When new one was tried, operator did not know to 'close the door' on the modem in order to power the card.&nbsp; Brent flew up and fixed.&nbsp; Missed 4 days of sampling.

*August 18*\--Lummi Bay deployment ended.&nbsp; Machine returned to NOAA.

_{+}Samish Bay:&nbsp;+_

*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; No CTD.&nbsp; Both machines have MFB and PCR.&nbsp; Media event was July 18.

Aug 14--Recover Gordon

Aug 17--Deploy (swap) NEO.

Sep 10--processing syringe servo motor has failed.&nbsp; Decision to run out remaining mission with archive only.

*Sep 16*\--NEO's mission ends.&nbsp; NOAA to recover and Roman/Kevan retrieved both machines Sep 25.

h4. {color:#ff00cc}ECOHAB/CANON--Monterey Bay{color}

*&nbsp;September 10, 2013*\-\- Deploy 2 ESP's in Monterey Bay.&nbsp; First time in southern part of bay.

'North'
ESP-Mack.&nbsp; Lat 36.9048, Long \-121.93659, Water depth 32m, Can depth 9.8m.

*Oct 11, 2013*\--Battery voltage dropped too low, and we had to end mission

'South'
ESP-Bruce. Lat 36.63908, Long \-121.87884, Water depth 60m, Can depth 4.8m

*Oct 10, 2013*--Found 'terminal fluid retention' on processing side--pulled an oring or some type of leak. Tried porting waste to Waste2 (known to be empty), but same results.  Final 3 samples to try and collect for SEM work.]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

h4. {color:#ff00cc}Puget Sound{color}

_{+}Lummi Bay:+_

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)

*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.&nbsp; Subsequent investigation found that modem card had been cancelled with T-Mobile due to NOAA miscommunication.&nbsp; When new one was tried, operator did not know to 'close the door' on the modem in order to power the card.&nbsp; Brent flew up and fixed.&nbsp; Missed 4 days of sampling.

*August 18*\--Lummi Bay deployment ended.&nbsp; Machine returned to NOAA.

_{+}Samish Bay:&nbsp;+_

*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; No CTD.&nbsp; Both machines have MFB and PCR.&nbsp; Media event was July 18.

Aug 14--Recover Gordon

Aug 17--Deploy (swap) NEO.

Sep 10--processing syringe servo motor has failed.&nbsp; Decision to run out remaining mission with archive only.

*Sep 16*\--NEO's mission ends.&nbsp; NOAA to recover and Roman/Kevan retrieved both machines Sep 25.

h4. {color:#ff00cc}ECOHAB/CANON--Monterey Bay{color}

*&nbsp;September 10, 2013*\-\- Deploy 2 ESP's in Monterey Bay.&nbsp; First time in southern part of bay.

'North'
ESP-Mack.&nbsp; Lat 36.9048, Long \-121.93659, Water depth 32m, Can depth 9.8m.

*Oct 11, 2013*\--Battery voltage dropped too low, and we had to end mission

'South'
ESP-Bruce. Lat 36.63908, Long \-121.87884, Water depth 60m, Can depth 4.8m

*Oct 10, 2013*-Found 'terminal fluid retention' on processing side-pulled an oring or some type of leak. Tried porting waste to Waste2 (known to be empty), but same results.  Final 3 samples to try and collect for SEM work.]]></property>
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<property name="body"><![CDATA[Instrument Level Control Loops
|| || Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Sampling Pump \\ | | | |
| 2 | Spool Valve actuator \\ | | | |
| 3 | Cylinder Rotate \\ | | | |
| 4 | Cartridge Actuator Alignment \\ | | | |
| 5 | Cartridge Actuator 1 \\ | | | |
| 6 | Cartridge Actuator 2 | | | |
| 7 | Cartridge Actuator 3 | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | |
| 9 | Cartridge Actuator Reagent Valve \\ | | | |
| 10 | A/M Clamp \\ | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | |
| 12 | A/M Hand-off Syringe \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
\\

Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | \\ | | | |
| 5 | \\ | | | |
| 6 | \\ | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
\\]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[Instrument Level Control Loops
|| || Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Sampling Pump \\ | | | |
| 2 | Spool Valve actuator \\ | | | |
| 3 | Cylinder Rotate \\ | | | |
| 4 | Cartridge Actuator Alignment\\ | | | |
| 5 | Cartridge Actuator 1\\ | | | |
| 6 | Cartridge Actuator 2 | | | |
| 7 | Cartridge Actuator 3 | | | |
| 8 | Cartridge Actuator Puck Evac\\ | | | |
| 9 | Cartridge Actuator Reagent Valve\\ | | | |
| 10 | A/M Clamp\\ | | | |
| 11 | A/M Clamp Radial Alignment\\ | | | |
| 12 | A/M Hand-off Syringe\\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | \\ | | | |
| 5 | \\ | | | |
| 6 | \\ | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
\\]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19072969</id>
<property name="body"><![CDATA[Instrument Level Control Loops
|| || Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Sampling Pump \\ | | | |
| 2 | Spool Valve actuator \\ | | | |
| 3 | Cylinder Rotate \\ | | | |
| 4 | Cartridge Actuator Alignment \\ | | | |
| 5 | Cartridge Actuator 1 \\ | | | |
| 6 | Cartridge Actuator 2 | | | |
| 7 | Cartridge Actuator 3 | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | |
| 9 | Cartridge Actuator Reagent Valve \\ | | | |
| 10 | A/M Clamp \\ | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | |
| 12 | A/M Hand-off Syringe \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
\\

Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
\\]]></property>
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<id name="id">19072967</id>
<property name="body"><![CDATA[Instrument Level Control Loops
|| || Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Sampling Pump \\ | | | |
| 2 | Spool Valve actuator \\ | | | |
| 3 | Cylinder Rotate \\ | | | |
| 4 | Cartridge Actuator Alignment \\ | | | |
| 5 | Cartridge Actuator 1 \\ | | | |
| 6 | Cartridge Actuator 2 | | | |
| 7 | Cartridge Actuator 3 | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | |
| 9 | Cartridge Actuator Reagent Valve \\ | | | |
| 10 | A/M Clamp \\ | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | |
| 12 | A/M Hand-off Syringe \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
\\

Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (1) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 ? \\ | | | |
| 5 | Heater 3 ? | | | |
| 6 | Heater 4 ? | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
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<property name="body"><![CDATA[Instrument Level

|| || Control Loops \\ || || Inputs \\ || Outputs || || || || || ||
| 1 \\ | Sampling Pump \\ | | | | | | | | |
| 2 | Spool Valve actuator \\ | | | | | | | | |
| 3 | Cylinder Rotate \\ | | | | | | | | |
| 4 | Cartridge Actuator Alignment \\ | | | | | | | | |
| 5 | Cartridge Actuator 1 \\ | | | | | | | | |
| 6 | Cartridge Actuator 2 | | | | | | | | |
| 7 | Cartridge Actuator 3 | | | | | | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | | | | | | |
| 9 | Cartridge Actuator Reagent Valve \\ | | | | | | | | |
| 10 | A/M Clamp \\ | | | | | | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | | | | | | |
| 12 | A/M Hand-off Syringe \\ | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |
\\

Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
\\]]></property>
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<id name="id">23199825</id>
<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

h4. {color:#ff00cc}Puget Sound{color}

_{+}Lummi Bay:+_

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)

*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.&nbsp; Subsequent investigation found that modem card had been cancelled with T-Mobile due to NOAA miscommunication.&nbsp; When new one was tried, operator did not know to 'close the door' on the modem in order to power the card.&nbsp; Brent flew up and fixed.&nbsp; Missed 4 days of sampling.

*August 18*\--Lummi Bay deployment ended.&nbsp; Machine returned to NOAA.

_{+}Samish Bay:&nbsp;+_

*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; No CTD.&nbsp; Both machines have MFB and PCR.&nbsp; Media event was July 18.

Aug 14--Recover Gordon

Aug 17--Deploy (swap) NEO.

Sep 10--processing syringe servo motor has failed.&nbsp; Decision to run out remaining mission with archive only.

*Sep 16*\--NEO's mission ends.&nbsp; NOAA to recover and Roman/Kevan retrieved both machines Sep 25.

h4. {color:#ff00cc}ECOHAB/CANON--Monterey Bay{color}

*&nbsp;September 10, 2013*\-\- Deploy 2 ESP's in Monterey Bay.&nbsp; First time in southern part of bay.

'North'
ESP-Mack.&nbsp; Lat 36.9048, Long \-121.93659, Water depth 32m, Can depth 9.8m.

'South'
ESP-Bruce. Lat 36.63908, Long \-121.87884, Water depth 60m, Can depth 4.8m]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

h4. {color:#ff00cc}Puget Sound{color}

_{+}Lummi Bay:+_

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)

*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.&nbsp; Subsequent investigation found that modem card had been cancelled with T-Mobile due to NOAA miscommunication.&nbsp; When new one was tried, operator did not know to 'close the door' on the modem in order to power the card.&nbsp; Brent flew up and fixed.&nbsp; Missed 4 days of sampling.

*August 18*\--Lummi Bay deployment ended.&nbsp; Machine returned to NOAA.

_{+}Samish Bay:&nbsp;+_

*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; No CTD.&nbsp; Both machines have MFB and PCR.&nbsp; Media event was July 18.

Aug 14--Recover Gordon

Aug 17--Deploy (swap) NEO.

Sep 10--processing syringe servo motor has failed.&nbsp; Decision to run out remaining mission with archive only.

*Sep 16*\--NEO's mission ends.&nbsp; NOAA to recover and Roman/Kevan retrieved both machines Sep 25.

h4. {color:#ff00cc}ECOHAB/CANON--Monterey Bay{color}

*&nbsp;September 10, 2013*\-\- Deploy 2 ESP's in Monterey Bay.&nbsp; First time in southern part of bay.

'North'
ESP-Mack.&nbsp; Lat 36.9048, Long \-121.93659, Water depth 32m, Can depth 9.8m.\\

'South'
ESP-Bruce. Lat 36.63908, Long \-121.87884, Water depth 60m, Can depth 4.8m

*Oct 10, 2013*\--Found 'terminal fluid retention' on processing side--pulled an oring or some type of leak. ]]></property>
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<id name="id">19073007</id>
<property name="body"><![CDATA[Instrument Level
|| || Control Loops&nbsp; || || Inputs \\ || Outputs || || || || || ||
| 1 \\ | Sampling Pump \\ | | | | | | | | |
| 2 | Spool Valve actuator \\ | | | | | | | | |
| 3 | Cylinder Rotate \\ | | | | | | | | |
| 4 | Cartridge Actuator Alignment \\ | | | | | | | | |
| 5 | Cartridge Actuator 1 \\ | | | | | | | | |
| 6 | Cartridge Actuator 2 | | | | | | | | |
| 7 | Cartridge Actuator 3 | | | | | | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | | | | | | |
| 9 | Cartridge Actuator Reagent Valve \\ | | | | | | | | |
| 10 | A/M Clamp \\ | | | | | | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | | | | | | |
| 12 | A/M Hand-off Syringe \\ | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |

|| || Discrete Actions || || \\ || Outputs || || || || || ||
| 1 \\ | Intake Select 1 \\ | | | | | | | | |
| 2 | Intake Select 2 \\ | | | | | | | | |
| 3 | Bulkhead valve (intake) \\ | | | | | | | | |
| 4 | Bulkhead valve (exhaust) | | | | | | | | |
| 5 | Cartridge Valve Actuator 1 \\ | | | | | | | | |
| 6 | Cylinder latch \\ | | | | | | | | |
| 7 | A/M Valve 1 \\ | | | | | | | | |
| 8 | A/M Valve 2 \\ | | | | | | | | |
| 9 | A/M Valve 3 | | | | | | | | |
| 10 | A/M Valve 4 | | | | | | | | |
| 11 | A/M Clamp \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |
\\

Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
\\]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]
# [Feb 16]
# Feb 23 \-\- Oceans Mtg., Portland
# [Mar 2]
# [Mar 9]
# Mar 16 \-\- Jim in S. Cal scouting.  John Ryan ran mtg.
# Mar 23
# Mar 30
# Apr 6 \-\- canceled in preparation for M0 deployment
# Apr 13
# Apr 20
# Apr 27 \--AbSciCon, League City TX
# [May 4]
# [May 11]
# [May 18]
# [Aug 24]
# [Sep 14]
# [Sep 21]
# Sep 28 \-\- Network deployment.&nbsp; no mtg
# Oct 5
# Oct 12
# Oct 19
# Oct 26 \-\- Chris S. @ WHOI, Jim at PICES
# [Nov 2]]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO. ]]></property>
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<id name="id">12550231</id>
<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
\\
\\]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Allison, Chris P, Elif, Roman, Doug P., Vanessa, John R, Jim

h3. Items:

1.&nbsp; Just discovered that McLane Pucks do not fit in puck-puller, and some have burrs.&nbsp; Doug has done cursory inspection and they seem to be at the limit of tolerance specifications.&nbsp; Will quarantine and inspect after we get Gordon on MARS.

2.&nbsp; Printer.&nbsp; Roman to try running printer without HEPA filter.&nbsp; Perkin-Elmer doesn't know what to suggest to do, even if they send someone.&nbsp; We are losing this one...

3.&nbsp; Gordon.&nbsp; in the middle of core/mfb testing.&nbsp; Some issues with RNALater being left in WCR pucks.&nbsp; Will do some testing on NEO before implementing in Gordon.&nbsp; Tonight to run BAC SHA MFB phase (low pressure).

3.&nbsp; Vanessa leaves saturday.&nbsp; She's running her MFB standards again and they are&nbsp; looking as good or better than pre-deployment\!

4.&nbsp; John R. reports that the LMO submission has gotten very favorable reviews.&nbsp; He will address and resubmit but things looking good for publication. ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris S., Doug, Brent, Jim, Roman

Absent: Chris P., Scott, Cheri, Wayne, Kevin\\

are computers fine?&nbsp; should we order more? ]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]
# [Feb 16]
# Feb 23 \-\- Oceans Mtg., Portland
# [Mar 2]
# [Mar 9]
# Mar 16 \-\- Jim in S. Cal scouting.  John Ryan ran mtg.
# Mar 23
# Mar 30
# Apr 6 \-\- canceled in preparation for M0 deployment
# Apr 13
# Apr 20
# Apr 27 \--AbSciCon, League City TX
# [May 4]
# [May 11]]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim B., Chris P, Roman M., Wayne R., Cheri E., Brent R., Chris S., Scott J., Doug P.

Absent:&nbsp; Cheri E.

h2. &nbsp;Issues:

\\

1.  Benthos Box:&nbsp; Supposedly being shipped today.&nbsp; Should arrive next week.&nbsp; Much testing needs to be done with it and acoustic release, as well as hull transducers on the flyer.

2.&nbsp; ISMS:&nbsp; being shipped to arrive May 19th.&nbsp; Peter changing a turbo pump, and we need to make wiring harness.&nbsp; mounting brackets already finished.&nbsp; Scott has cabling which needs potting.

3.&nbsp; Light seal issues on current cores was not discussed.

h2. &nbsp;Methane cruise

1.&nbsp; Much discussion over puck make-up necessary for this mission and pre-mission testing.&nbsp; Here is plan as of 13May2010. map necessary.&nbsp; Chris P. created
\\

\\
2.&nbsp; CTD's:&nbsp; One must be sent back to Seabird and therefore will be  returned with the newer firmware.&nbsp; We must get Bob Herlein to do work.

3.&nbsp; Roman to disassemble and do forensics on Bruce and Mack.&nbsp; Start  Monday.

4.&nbsp; Cheri to visit McLane May 17.

5.&nbsp; Methane Mound cruise is gelling.&nbsp;A.&nbsp; Load WF July 21; shove off  July 22

B.&nbsp; begin return to Moss Landing July 27; arrive July 28
LOCATION:a.&nbsp; WF will be in Los Angles Harbor, Berth 262 near Wharf and  Tuna: &nbsp;WF location

b.&nbsp; Discussion ensued; we will use Benthos modem.&nbsp; Deckbox should  arrive late this week.

c.&nbsp; ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim B., Chris P, Roman M., Wayne R., Cheri E., Brent R., Chris S., Scott J., Doug P.

Absent:&nbsp; Cheri E.

h2. &nbsp;Issues:

\\

1.  Benthos Box:&nbsp; Supposedly being shipped today.&nbsp; Should arrive next week.&nbsp; Much testing needs to be done with it and acoustic release, as well as hull transducers on the flyer.

2.&nbsp; ISMS:&nbsp; being shipped to arrive May 19th.&nbsp; Peter changing a turbo pump, and we need to make wiring harness.&nbsp; mounting brackets already finished.&nbsp; Scott has cabling which needs potting.

3.&nbsp; Light seal issues on current cores was not discussed.

h2. &nbsp;Methane cruise

1.&nbsp; Much discussion over puck make-up necessary for this mission and pre-mission testing.&nbsp; [Here|https://oceana.mbari.org/confluence/plugins/tinymce/wysiwyg-insertlink-draft-attachmentstab.action?currentspace=ESPAPP&formname=createpageform&fieldname=wysiwygcontent&draftType=page&spaceKey=ESPAPP&mode=attachments#|Puck usage plan] is plan as of 13May2010. map necessary.&nbsp; Chris P. created
\\

\\
2.&nbsp; CTD's:&nbsp; One must be sent back to Seabird and therefore will be  returned with the newer firmware.&nbsp; We must get Bob Herlein to do work.

3.&nbsp; Roman to disassemble and do forensics on Bruce and Mack.&nbsp; Start  Monday.

4.&nbsp; Cheri to visit McLane May 17.

5.&nbsp; Methane Mound cruise is gelling.&nbsp;A.&nbsp; Load WF July 21; shove off  July 22

B.&nbsp; begin return to Moss Landing July 27; arrive July 28
LOCATION:a.&nbsp; WF will be in Los Angles Harbor, Berth 262 near Wharf and  Tuna: &nbsp;WF location

b.&nbsp; Discussion ensued; we will use Benthos modem.&nbsp; Deckbox should  arrive late this week.

c.&nbsp; ]]></property>
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<property name="body"><![CDATA[h1. Discussion of 18 Feb 2010

Luke Coletti, Doug Pargett, Jim Birch
# &nbsp;For July, 2010 WF cruise, ESP team will use Johnson lab 1Km housing.&nbsp; There were some issues with the last time it was used; weird readings--discussion ensued as to why readings not normal.
# Doug to draw up plans for pressure housing based on original aluminum design, keeping original diameter, using 2 radial o-rings to seal end caps.
# Doug will draw up plans for probe head opening using the actual probe he has, and getting rid of the current goofy SAE opening.
# We will make 2 Ti housings; ESP pays for 1, Johnson lab pays for 1.
# Eventually we will power the deep ISUS from our Deep-Sea Power and light battery stack, which will allow recharging if needed.&nbsp; But for July we'll use Luke's battery pack (especially since it's such a short deployment).]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim B., Chris P, Roman M., Wayne R., Cheri E., Brent R., Julie R., Scott J.

Absent:&nbsp; Chris Scholin, Doug Pargett.

h2. &nbsp;Issues:

\\

1.&nbsp; NEO preparationsball screw has been replaced with new one.&nbsp; Reagents corrected.&nbsp; CTD compatibility to be dealt with on the deck by 'hot-swapping' with one that works on MOE.&nbsp; Pressure differential error:&nbsp; must be the sensor.&nbsp; The two have very different response slopes, so will replace with a new pressure gauge. Discussion ensued on what exactly the logs looked like.&nbsp; Brent to look at the first deployment log.&nbsp; {color:#ff0000}We must look at temperature effects on pressure gauges.{color}

\\
2.&nbsp; CTD's:&nbsp; One must be sent back to Seabird and therefore will be returned with the newer firmware.&nbsp; We must get Bob Herlein to do work.

3.&nbsp; Roman to disassemble and do forensics on Bruce and Mack.&nbsp; Start Monday.

4.&nbsp; Cheri to visit McLane May 17.

5.&nbsp; Methane Mound cruise is gelling.&nbsp;A.&nbsp; Load WF July 21; shove off July 22

B.&nbsp; begin return to Moss Landing July 27; arrive July 28

LOCATION:a.&nbsp; WF will be in Los Angles Harbor, Berth 262 near Wharf and Tuna: &nbsp;[WF location|http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&msid=111102629856882203099.000485df2087907222856&ll=33.768636,-118.459546&spn=0.650709,0.787582&z=11|WF in S. Cal for Methane Mound]\\]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim B., Chris P, Roman M., Wayne R., Cheri E., Brent R., Julie R., Scott J.

Absent:&nbsp; Chris Scholin, Doug Pargett.

h2. &nbsp;Issues:

\\

1.&nbsp; NEO preparationsball screw has been replaced with new one.&nbsp; Reagents corrected.&nbsp; CTD compatibility to be dealt with on the deck by 'hot-swapping' with one that works on MOE.&nbsp; Pressure differential error:&nbsp; must be the sensor.&nbsp; The two have very different response slopes, so will replace with a new pressure gauge. Discussion ensued on what exactly the logs looked like.&nbsp; Brent to look at the first deployment log.&nbsp; {color:#ff0000}We must look at temperature effects on pressure gauges.{color}\\ &nbsp;
\\]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]
# [Feb 16]
# Feb 23 \-\- Oceans Mtg., Portland
# [Mar 2]
# [Mar 9]
# Mar 16 \-\- Jim in S. Cal scouting.  John Ryan ran mtg.
# Mar 23
# Mar 30
# Apr 6 \-\- canceled in preparation for M0 deployment
# Apr 13
# Apr 20
# Apr 27 \--AbSciCon, League City TX
# [May 4]]]></property>
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<property name="body"><![CDATA[Distribution list as of 10 May 2010:
\\
\\
|| MFB || PCR Module # || on Core || who gets? || ||
| tombstone | 5 \\ | NEO \\ | MBARI | |
| MFB1 | 1 | Moe | MBARI | |
| MFB2 | \\ | Betty | MBARI | |
| MFB3 | 4 | Gordon | MBARI | |
| MFB4 | 7 \\ | | CMORE | |
| MFB5 | 8 | | U. of Ga \\ | |
| MFB6 | \\ | | Stanford | \\ |
| MFB7 | | | Harvard/Girgius | |
| MFB8 | none | | Harban's | |
| MFB9 | 13 \\ | | Caltech/Orphan | |
| MFB10 | 11 | | SCCWRP | |
| {color:#3366ff}&nbsp;MFB11{color} | 12 | | MBARI | under construction \\ |
| | | | | |
| | Spare: | | | |
| | 14 | | | |
| | Broken?: | | | |
| | 3 | | was originally on Tombstone, but moved #9 there for M0 deployment. Not enough sensitivity.&nbsp; \\ | |
| | 10 | | removed from MFB6.&nbsp; Bleach leak caused flakey connector. \\ | |
| | 9 | | removed from tombstone.&nbsp; Eradict diode readings \\ | |]]></property>
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<property name="body"><![CDATA[Distribution list as of 05 Apr 2010:
\\
\\
|| MFB || PCR Module # || on Core || who gets? || ||
| tombstone | 5 \\ | NEO \\ | MBARI | |
| MFB1 | 1 | Moe | MBARI | |
| MFB2 | \\ | Betty | MBARI | |
| MFB3 | 4 | Gordon | MBARI | |
| MFB4 | 7 \\ | | CMORE | |
| MFB5 | 8 | | U. of Ga \\ | |
| MFB6 | \\ | | Stanford | \\ |
| MFB7 | | | Harvard/Girgius | |
| MFB8 | none | | Harban's | |
| MFB9 | 13 \\ | | Caltech/Orphan | |
| MFB10 | 11 | | SCCWRP | |
| {color:#3366ff}&nbsp;MFB11{color} | 12 | | MBARI | under construction \\ |
| | | | | |
| | Spare: | | | |
| | 14 | | | |
| | Broken?: | | | |
| | 3 | | was originally on Tombstone, but moved #9 there for M0 deployment. Not enough sensitivity.&nbsp; \\ | |
| | 10 | | removed from MFB6.&nbsp; Bleach leak caused flakey connector. \\ | |
| | 9 | | removed from tombstone.&nbsp; Eradict diode readings \\ | |]]></property>
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<property name="body"><![CDATA[Distribution list as of 05 Apr 2010:
\\
\\
|| MFB || PCR Module # || on Core || who gets? || ||
| tombstone | 5 \\ | NEO \\ | MBARI | |
| MFB1 | 1 | Moe | MBARI | |
| MFB2 | \\ | Betty | MBARI | |
| MFB3 | 4 | Gordon | MBARI | |
| MFB4 | 7 \\ | | CMORE | |
| MFB5 | 8 | | U. of Ga \\ | |
| MFB6 | \\ | | Stanford | \\ |
| MFB7 | | | Harvard/Girgius | |
| MFB8 | none | | Harban's | |
| MFB9 | 13 \\ | | Caltech/Orphan | |
| MFB10 | 11 | | SCCWRP | |
| {color:#3366ff}&nbsp;MFB11{color} | 12 | | MBARI | under construction \\ |
| | | | | |
| | Spare: | | | |
| | 14 | | | |
| | 3 | | was originally on Tombstone, but moved #9 there for M0 deployment \\ | |
| | 10 | | removed from MFB6.&nbsp; Bleach leak caused flakey connector.\\ | |
| | 9 | | removed from tombstone.&nbsp; Eradict diode readings\\ | |]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]
# [May 20]
# [May 27]
# June 3
# June 10
# [June 17]
# June 24 \-\- Scott led
# July 1 \-\- Doug led
# [July 8]
# Jul 15 \--Preparation for Methane cruise
# Jul 22 \--Methane cruise
# Jul 29 \--Methane cruise
# [Aug 5]
# [Aug 12]
# [Aug 19]
# [Aug 26]
# [Sep 2]
# [Sep 9] \--CANON cruise, Scholin in England
# [Sep 16]
# Sep 12 \--prep for triple deployment
# [Sep 30]]]></property>
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<property name="body"><![CDATA[Present: Jim, Scott, Doug, Bruce K., Roman, Brent, Chris P


Absent: Chris S., Julie, John R.

h3. Issues:

* Much Discussion on schedule of Gordon and D-ESP Prep.&nbsp; Current calendar is [here|https://oceana.mbari.org/confluence/plugins/tinymce/wysiwyg-insertlink-draft-uploadfile.action#|MARS 2010 Calendar].

h6.

* Jose working on 48V switch-over for ISMS integration.&nbsp; Must check with him to see what instructions he was left from Scott.
* Need to call Pete about his ISMS plans.
* Brent working rest of year on integration of newer version of Ruby.
* Also wants to develop .JPEG thumbnails, that could be easily sent over Iridium.&nbsp; This has it's drawbacks, as they can't be analyzed, but otherwise 70MB/30-day deployment is too costly using Iridium.
* Roman to work on array printer.&nbsp; We need BAC arrays.
* The new CTD sensor has an Oxygen sensor; means we need to tweak the new driver.&nbsp; Brent working on this.]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound.

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deployment----MOE @ M0-\- w/PCR, ISUS.&nbsp; 121 54.11 E; 36 50.10 N.&nbsp; 72m water depth
{color:#33cc00}September 29{color} \-\- Bruce @ offshore (SC) with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; 36 53.75&nbsp; \-122 2.75. 52m water depth.&nbsp; Weight measurements are [HERE|ESPAPP:Weight Calculations for BRUCE|mooring weights].
{color:#33ff00}September 28{color} \-\- Mack @ bight \--&nbsp; no ISUS. no PCR; Using RNALater as preservative.&nbsp; 36 55.95&nbsp; \-121 55.35.&nbsp; 19m water depth.&nbsp; (Lat/Long are from Aaron Gregg after deployment.)]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound.

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deploymentMOE @ M0-\- w/PCR, ISUS.&nbsp; 72m water depth
{color:#33cc00}September 29{color} \-\- Bruce @ offshore (SC) with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; 36 53.75&nbsp; \-122 2.75. 52m water depth.&nbsp; Weight measurements are [HERE|ESPAPP:Weight Calculations for BRUCE|mooring weights].
{color:#33ff00}September 28{color} \-\- Mack @ bight \--&nbsp; no ISUS. no PCR; Using RNALater as preservative.&nbsp; 36 55.95&nbsp; \-121 55.35.&nbsp; 19m water depth.&nbsp; (Lat/Long are from Aaron Gregg after deployment.)]]></property>
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<property name="body"><![CDATA[This is the documentation to detail out the design of the state representation interface between the GUI application and the instrument itself.  This interface will allow the GUI (and other applications) to get information about the current state of the various components of the ESP.

Some details about the interface:
# The ESP application (server) shall listen on a fixed TCP socket.
# Any number clients can connect to this socket, each thereby opening a separate, private, bidirectional, ASCII connection to the ESP server.
# The server will respond to the following client commands:
## List all available states
### Each state is identified by a short symbolic (ASCII) name.
## Retrieve metadata for subset of those states and subscribe to them
### Elements in lists of states are separated with commas
#### There is no whitespace between list elements
### The order of the elements in state lists determine the ordering in reporting state vectors described below.
### Metadata shall include:
#### Description  e.g.  Storage carousel
#### sprintf format string  e.g.  %.2fml
#### range  (min and max expected values)
{note}hardware failures may cause reported values to be out of range
{note}
#### map of sybolically labeled positions, each on a line of this format:
{noformat}
  <numeric position>,<symbolic label>,<alias1>,<alias2>,<aliasN>
{noformat}
## Subscribe to updates on (only) the specified states
{note}This limits subsequent state updates to just those listed by their symbolic names. This message also determines the ordering of states in vectors described below.
{note}
## Refresh all subscribed states
{note}All the subscribed states are sent to the client in the order in which they were listed in the most recent subscribe or retrieve metadata message.
{noformat}
<timestamp?  seconds since epoch??>
<new value[0]>{,optional additional info like current, pwm%, etc. (may be ignored)}
<new value[1]>{,optional additional info like current, pwm%, etc.}
...
<new value[n-1]>{,optional additional info like current, pwm%, etc.}
{noformat}
where n is the number of states subscribed.  This establishes a baseline from which subsequent state changes are reported.
{note}
## Request C more changed state updates at maximum rate one per t tenths of seconds.
{note}
* The client tells the server it is ready to receive C more state change responses and that the server may emit these at a rate no faster than one every t tenths of a second.
* A client wishing to continuously monitor state should send a new request shortly *before* the last update (as allowed by the previous request) has been received. If C is kept small (say 10 or so), this mechanism will ensure that update messages don't back up on the networking queue, while avoiding paying any network latency penalty.  (Similar to TCP's sliding window mechanism)
* The client can stop updates by requesting 0 more at some arbitrary rate.
* Only those states whose values changed since the last update will be sent
* Format will be a list of lines, each of the form:
{noformat}
<index>,<new value>
{noformat}
where:
* index = an integer from 0 to n-1 where n is the number of subscribed states
* new value = number conforming to the state's sprintf format string (note that the unit suffix will be omitted, i.e. 0.2 not 0.2ml)
{note}
{note:title=Notes for Brent}Normally, all I2C messages between the Linux host and the dwarves are logged. However, this protocol will require continuous polling of all the subscribed dwarves' raw positions.  Nothing else currently does anything like this (by design\! :-) . Clearly, such messages should not be logged.  Further, it may be necessary to add an I2C message to the dwarf firmware that queries raw position only.  The existing full status poll message returns lots of extraneous engineering info like velocity, electrical current, etc.
{note}]]></property>
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<property name="body"><![CDATA[This is the documentation to detail out the design of the state representation interface between the GUI application and the instrument itself.  This interface will allow the GUI (and other applications) to get information about the current state of the various components of the ESP.

Some details about the interface:
# The ESP application (server) shall listen on a fixed TCP socket.
# Any number clients can connect to this socket, each thereby opening a separate, private, bidirectional, ASCII connection to the ESP server.
# The server will respond to the following client commands:
## List all available states
### Each state is identified by a short symbolic (ASCII) name.
## Retrieve metadata for subset of those states and subscribe to them
### Elements in lists of states are separated with commas
####  There is no whitespace between list elements
### The order of the elements in state lists determine the ordering in reporting state vectors described below.
### Metadata shall include:
#### Description  e.g.  Storage carousel
#### sprintf format string  e.g.  %.2fml
#### range  (min and max expected values)
{note}hardware failures may cause reported values to be out of range
{note}
#### map of sybolically labeled positions, each on a line of this format:
{noformat}
  <numeric position>,<symbolic label>,<alias1>,<alias2>,<aliasN>
{noformat}
## Subscribe to updates on (only) the specified states
{note}This limits subsequent state updates to just those listed by their symbolic names. This message also determines the ordering of states in vectors described below.
{note}
## Refresh all subscribed states
{note}All the subscribed states are sent to the client in the order in which they were listed in the most recent subscribe or retrieve metadata message.
{noformat}
<timestamp?  seconds since epoch??>
<new value[0]>
<new value[1]>
...
<new value[n-1]>
{noformat}
where n is the number of states subscribed.  This establishes a baseline from which subsequent state changes are reported.
{note}
## Request C more changed state updates at maximum rate one per t tenths of seconds.
{note}
* The client tells the server it is ready to receive C more state change responses and that the server may emit these at a rate no faster than one every t tenths of a second.
* A client wishing to continuously monitor state should send a new request shortly *before* the last update (as allowed by the previous request) has been received. If C is kept small (say 10 or so), this mechanism will ensure that update messages don't back up on the networking queue, while avoiding paying any network latency penalty.  (Similar to TCP's sliding window mechanism)
* The client can stop updates by requesting 0 more at some arbitrary rate.
* Only those states whose values changed since the last update will be sent
* Format will be a list of lines, each of the form:
{noformat}
<index>,<new value>
{noformat}
where:
* index = an integer from 0 to n-1 where n is the number of subscribed states
* new value = number conforming to the state's sprintf format string (note that the unit suffix will be omitted, i.e. 0.2 not 0.2ml)
{note}
{note:title=Notes for Brent}
Normally, all I2C messages between the Linux host and the dwarves are logged. However, this protocol will require continuous polling of all the subscribed dwarves' raw positions.  Nothing else currently does anything like this (by design\! :-) . Clearly, such messages should not be logged.  Further, it may be necessary to add an I2C message to the dwarf firmware that queries raw position only.  The existing full status poll message returns lots of extraneous engineering info like velocity, electrical current, etc.
{note}]]></property>
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<property name="body"><![CDATA[Present: Jim, Scott, Doug, Bruce K., Roman, Brent, Chris P

Absent: Chris S., Julie, John R.

h3. Issues:

* Much Discussion on schedule of Gordon and D-ESP Prep.&nbsp; Current calendar is [|MARS 2010 Calendar].

h6.

* Jose working on 48V switch-over for ISMS integration.&nbsp; Must check with him to see what instructions he was left from Scott.
* Need to call Pete about his ISMS plans.
* Brent working rest of year on integration of newer version of Ruby.
* Also wants to develop .JPEG thumbnails, that could be easily sent over Iridium.&nbsp; This has it's drawbacks, as they can't be analyzed, but otherwise 70MB/30-day deployment is too costly using Iridium.
* Roman to work on array printer.&nbsp; We need BAC arrays.
* The new CTD sensor has an Oxygen sensor; means we need to tweak the new driver.&nbsp; Brent working on this.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris S., Chris P., Roman, Julie, John, Jim

Absent: Bill U.

{color:#3300ff}1. Updates:{color}\\
* {color:#3300ff}Array printing update{color}
** computer died this weekend.&nbsp; New (old) one is coming today or tomorrow.&nbsp; Perkin-Elmer sending tech to set it up and load driver but they will not help re-calibrate tips if that needed.&nbsp; Very disappointed with service they have provided for the price we've paid.&nbsp;
** We are out of BAC arrays; these are first priority for Roman.&nbsp; There is also much work to recalibrate machine and re-create puck maps.

* {color:#3300ff}Cheri headed to McLane on Sunday for the week.{color}
** She will take 2 SH1, 1 LAF, 1WCR pucks and filters/supports.&nbsp; Roman will help get those together.

* {color:#3300ff}NEO deployment next week{color}
** (correct) reagents loading today.
** ball screw has been replaced.
** will hot-swap CTD on ship, so older CTD with current working driver will be in use.&nbsp; Bob Herlien can write new driver, but not until August.
** Pressure sign inversion still to be fixed.&nbsp; Email sent to Scott to band-aid by placing different resistor on sensor board.

* {color:#3300ff}Check-out/fix broken PCR modules{color}
** We will assemble data on the malfunctioning of each module and submit to John D @ LLNL and ask for help.&nbsp; This will occur after the flip.

* {color:#3300ff}John R. Paper progress{color}
** John has sifted through contextual data and skimmed the nuggets of interpretability.&nbsp; Seems like a very nice story is emerging.&nbsp; He will send figures and outline draft of paper this week.

* {color:#3300ff}Chris P. paper progress{color}
** Chris continues writing and gave review of the figures she's settled on.
** still looking at submission to PNAS or Applied Env. Micro.

* {color:#3300ff}Methane Mound Cruise{color}
** Much discussion on the timeline of the cruise and when things needed to be done.&nbsp; Chris P. had valuable input into when she could assist.&nbsp; The schedule still is somewhat flexible. ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris S., Chris P., Roman, Julie, John, Jim

Absent: Bill U.

{color:#3300ff}1. Updates:{color}\\
* {color:#3300ff}Array printing update{color}
** computer died this weekend.&nbsp; New (old) one is coming today or tomorrow.&nbsp; Perkin-Elmer sending tech to set it up and load driver but they will not help re-calibrate tips if that needed.&nbsp; Very disappointed with service they have provided for the price we've paid.&nbsp;
** We are out of BAC arrays; these are first priority for Roman.&nbsp; There is also much work to recalibrate machine and re-create puck maps.

* {color:#3300ff}Cheri headed to McLane on Sunday for the week.{color}
** She will take 2 SH1, 1 LAF, 1WCR pucks and filters/supports.&nbsp; Roman will help get those together.

* {color:#3300ff}NEO deployment next week{color}
** (correct) reagents loading today.
** ball screw has been replaced.
** will hot-swap CTD on ship, so older CTD with current working driver will be in use.&nbsp; Bob Herlien can write new driver, but not until August.
** Pressure sign inversion still to be fixed.&nbsp; Email sent to Scott to band-aid by placing different resistor on sensor board.

* {color:#3300ff}Check-out/fix broken PCR modules{color}
** We will assemble data on the malfunctioning of each module and submit to John D @ LLNL and ask for help.&nbsp; This will occur after the flip.

* {color:#3300ff}Bruce/Mack{color}
** Mack had an extra puck in one tube, due to the machine being stopped when the hand was gripping over the carousel.&nbsp; We were lucky it fell into tube 5 so it could continue a HAB run from tube 4.
** Bruce to be opened tomorrow.&nbsp;
** We will appeal to Support Engineering to help in mooring cleaning and preparation.

* {color:#0000ff}John R. Paper progress{color}
** John has sifted through contextual data and skimmed the nuggets of interpretability.&nbsp; Seems like a very nice story is emerging.&nbsp; He will send figures and outline draft of paper this week.

* {color:#3300ff}Chris P. paper progress{color}
** Chris continues writing and gave review of the figures she's settled on.
** still looking at submission to PNAS or Applied Env. Micro.

* {color:#3300ff}Methane Mound Cruise{color}
** Much discussion on the timeline of the cruise and when things needed to be done.&nbsp; Chris P. had valuable input into when she could assist.&nbsp; The schedule still is somewhat flexible.]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound (33.799, \-118.647).

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deployment--MOE @ M0-\- w/PCR, ISUS.&nbsp; 121 54.11 E; 36 50.10 N.&nbsp; 72m water depth
{color:#33cc00}September 29{color} \-\- Bruce @ offshore (SC) with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; 36 53.75&nbsp; \-122 2.75. 52m water depth.&nbsp; Weight measurements are [HERE|ESPAPP:Weight Calculations for BRUCE|mooring weights].
{color:#33ff00}September 28{color} \-\- Mack @ bight \--&nbsp; no ISUS. no PCR; Using RNALater as preservative.&nbsp; 36 55.95&nbsp; \-121 55.35.&nbsp; 19m water depth.&nbsp; (Lat/Long are from Aaron Gregg after deployment.)]]></property>
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<property name="body"><![CDATA[Distribution list as of 14 June 2010:
\\
\\
|| MFB || PCR Module # || on Core || who gets? || ||
| tombstone | 5 \\ | NEO \\ | MBARI | |
| MFB1 | 1 | Moe | MBARI | |
| MFB2 | 12 \\ | Betty | MBARI | |
| MFB3 | 4 | Gordon | MBARI | |
| MFB4 | 7 \\ | | CMORE | |
| MFB5 | \\ | | U. of Ga \\ | |
| MFB6 | 8 \\ | | Stanford | \\ |
| MFB7 | | | Harvard/Girgius | |
| MFB8 | none | | Harban's | |
| MFB9 | 13 \\ | | Caltech/Orphan | |
| MFB10 | 11 | | SCCWRP | |
| {color:#3366ff}&nbsp;MFB11{color} | 14\\ | | MBARI | under construction \\ |
| | | | | |
| | Spare: | | | |
| | none\\ | | | |
| | Broken?: | | | |
| | 3 | | was originally on Tombstone, but moved #9 there for M0 deployment. Not enough sensitivity.&nbsp; \\ | |
| | 10 | | removed from MFB6.&nbsp; Bleach leak caused flakey connector. \\ | |
| | 9 | | removed from tombstone.&nbsp; Erratic diode readings \\ | |]]></property>
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<property name="body"><![CDATA[Present: Jim, Scott, Doug, Bruce K., Roman, Brent, Chris P

Absent: Chris S., Julie, John R.

h3. Issues:

* Much Discussion on schedule of Gordon and D-ESP Prep.&nbsp; Current calendar is [MARS 2010 Calendar|^MARS 2010 calendar.pdf].

h6.

* Jose working on 48V switch-over for ISMS integration.&nbsp; Must check with him to see what instructions he was left from Scott.
* Need to call Pete about his ISMS plans.
* Brent working rest of year on integration of newer version of Ruby.
* Also wants to develop .JPEG thumbnails, that could be easily sent over Iridium.&nbsp; This has it's drawbacks, as they can't be analyzed, but otherwise 70MB/30-day deployment is too costly using Iridium.
* Roman to work on array printer.&nbsp; We need BAC arrays.
* The new CTD sensor has an Oxygen sensor; means we need to tweak the new driver.&nbsp; Brent working on this.]]></property>
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<property name="body"><![CDATA[Present: Jim, Scott, Doug, Bruce K., Roman, Brent, Chris P

Absent: Chris S., Julie, John R.

h3. Issues:

* Much Discussion on schedule of Gordon and D-ESP Prep.&nbsp; Current calendar is [MARS 2010 Calendar v2|^MARS 2010 calendar v2.pdf].

h6.

* Jose working on 48V switch-over for ISMS integration.&nbsp; Must check with him to see what instructions he was left from Scott.
* Need to call Pete about his ISMS plans.
* Brent working rest of year on integration of newer version of Ruby.
* Also wants to develop .JPEG thumbnails, that could be easily sent over Iridium.&nbsp; This has it's drawbacks, as they can't be analyzed, but otherwise 70MB/30-day deployment is too costly using Iridium.
* Roman to work on array printer.&nbsp; We need BAC arrays.
* The new CTD sensor has an Oxygen sensor; means we need to tweak the new driver.&nbsp; Brent working on this.]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]
# [May 20]
# [May 27]
# June 3
# June 10
# [June 17]
# June 24 \-\- Scott led
# July 1 \-\- Doug led
# [July 8]
# Jul 15 \--Preparation for Methane cruise
# Jul 22 \--Methane cruise
# Jul 29 \--Methane cruise
# [Aug 5]
# [Aug 12]
# [Aug 19]
# [Aug 26]
# [Sep 2]
# [Sep 9] \--CANON cruise, Scholin in England
# [Sep 16]
# Sep 12 \--prep for triple deployment
# [Sep 30]
# [Oct 7]
# Oct 14
# Oct 21
# Oct 28 \--Chris S @ WHOI, Jim at Pices
# Nov 4]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound.

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deployment\-\-MOE @ M0-- w/PCR, ISUS.&nbsp; 121 54.11 E; 36 50.10 N.&nbsp; 72m water depth
{color:#33cc00}September 29{color} \-\- Bruce @ offshore (SC) with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; 36 53.75&nbsp; \-122 2.75. 52m water depth.&nbsp; Weight measurements are [HERE|ESPAPP:Weight Calculations for BRUCE|mooring weights].
{color:#33ff00}September 28{color} \-\- Mack @ bight \--&nbsp; no ISUS. no PCR; Using RNALater as preservative.&nbsp; 36 55.95&nbsp; \-121 55.35.&nbsp; 19m water depth.&nbsp; (Lat/Long are from Aaron Gregg after deployment.)]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]
# [Feb 16]
# Feb 23 \-\- Oceans Mtg., Portland
# [Mar 2]
# [Mar 9]
# Mar 16 \-\- Jim in S. Cal scouting.  John Ryan ran mtg.
# Mar 23
# Mar 30
# Apr 6 \-\- canceled in preparation for M0 deployment
# Apr 13
# Apr 20
# Apr 27 \--AbSciCon, League City TX
# [May 4]
# [May 11]
# [May 18]
# [Aug 24]
# [Sep 14]
# [Sep 21]]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]
# [May 20]
# [May 27]
# June 3
# June 10
# [June 17]
# June 24 \-\- Scott led
# July 1 \-\- Doug led
# [July 8]
# Jul 15 \--Preparation for Methane cruise
# Jul 22 \--Methane cruise
# Jul 29 \--Methane cruise
# [Aug 5]
# [Aug 12]
# [Aug 19]
# [Aug 26]
# [Sep 2]
# [Sep 9] \--CANON cruise, Scholin in England
# [Sep 16]
# Sep 12 \--prep for triple deployment
# [Sep 30]
# [Oct 7]]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

h4. {color:#ff00cc}Puget Sound{color}

_{+}Lummi Bay:+_

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)

*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.&nbsp; Subsequent investigation found that modem card had been cancelled with T-Mobile due to NOAA miscommunication.&nbsp; When new one was tried, operator did not know to 'close the door' on the modem in order to power the card.&nbsp; Brent flew up and fixed.&nbsp; Missed 4 days of sampling.

*August 18*\--Lummi Bay deployment ended.&nbsp; Machine returned to NOAA.

_{+}Samish Bay:&nbsp;+_

*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; No CTD.&nbsp; Both machines have MFB and PCR.&nbsp; Media event was July 18.

Aug 14--Recover Gordon

Aug 17--Deploy (swap) NEO.

Sep 10--processing syringe servo motor has failed.&nbsp; Decision to run out remaining mission with archive only.

*Sep 16*\--NEO's mission ends.&nbsp; NOAA to recover and Roman/Kevan retrieved both machines Sep 25.

h4. {color:#ff00cc}ECOHAB/CANON--Monterey Bay{color}

*&nbsp;September 10, 2013*\-\- Deploy 2 ESP's in Monterey Bay.&nbsp; First time in southern part of bay.

{color:#cc3366}*'North'*{color}
ESP-Mack.&nbsp; Lat 36.9048, Long \-121.93659, Water depth 32m, Can depth 9.8m.

*Oct 11, 2013*\--Battery voltage dropped too low, and we had to end mission

{color:#cc3366}*'South'*{color}
ESP-Bruce. Lat 36.63908, Long \-121.87884, Water depth 60m, Can depth 4.8m

*Oct 10, 2013*\-Found 'terminal fluid retention' on processing side-pulled an oring or some type of leak. Tried porting waste to Waste2 (known to be empty), but same results.  Final 3 samples to try and collect for SEM work.]]></property>
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<property name="body"><![CDATA[h2.


h1. We currently (12-2012) have three Melo trackers

{color:#006600}The Melo is the 'watch-circle' warning transponder for surface moorings.{color}\\

IMEI numbers:

h3. *300034012090780&nbsp; (purchased June, 2011)*


h3. 300234060016190&nbsp; (serial # 122)&nbsp;&nbsp; (both purchased Dec, 2012)


h3. 300234060014550 (serial # 123)

\\

User's Manuals
# [Quick Start Guide v1.2|^Xeos_Melo_manual-1.pdf|quick start]
# [User Manual v1.5|^Melo_User_Manual _watch_circle_V1.5.pdf|Full Manual]
# [Watch Circle Console User Manual v2.1|^Xeos_Melo_manual-3.pdf|watch circle]\\
# [Xeos pricing changes as of Jan 2013|^Xeos_Iridium_BillingProcess_CustomerLetter.pdf]]]></property>
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<property name="body"><![CDATA[h3.


h3. Tech Transfer

* Although only calibrated to room temperature, Neo is ready to make lysate.&nbsp; After a positive result, will run DA tests, then remove those reagents and finish cold and hot calibrations.&nbsp; Then give to science for exercise.
* Moe: waiting on boards, motors, and machined parts.&nbsp; Scott pushing to have boards finished by early July.
* Must determine where AIV valve will go when merging MFB on Moe core, and update solid model ({color:#ff0000}To Do: Addie/Cheri/Scott/Chris S){color}
* &nbsp;

h3. MFB

* Despite repeated failures of the MFB, Chris S. states, "we are homing in on it...
* cc Addie any emails from LLNL
* Must address changing of power supply of heater/MFB/extraction (Action:&nbsp; Addie & Scott)
* Next week will move MFB to Bldg A lab and then run stink-water T/W/Th after Chris P returns from Microbiology mtg.

h3. Software

* Mack's hand has stuck twice during the current deployment (now on day 8) and Brent thinks it's getting worse.&nbsp;
* Must get more people on the beeper system, and he will train Cheri & Scott how to fix.
* Brent will stay on Kevin about GUI development, though next deployment is in Fall.

h3. DWSM

* CDR will be 10am Tuesday, June 10.&nbsp; Will invite same people that came to PDR.&nbsp; Jim will get room.

h3. Other Items

* Laid out and discussed plans for 2009.&nbsp; Plans concentrated in 4 areas:
** development of 4K system, culminating in cruise to Axial seamount in Q3.
** bench testing of MFB/PCR either here or in S. Cal as part of the EPA epidemiological study.
** pier deployments in S. Cal for water quality
** drifter study culminating in HI deployment, again in Q3]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]]]></property>
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<property name="body"><![CDATA[Present: Scott, Doug, Addie, Kevin, Jim, Cheri, Brent, Wayne

Absent:&nbsp; Chris S (in China)

h3. Deployment Update

* &nbsp;

h3. Machine Builds

* &nbsp;Moe now has GG's harmonic drive part of the hand.&nbsp; Cheri noticed that GG's lower hand is sticky; could be slider, could be bad motor.
* Bruce leak.&nbsp; Found that o-rings in processing clamp were noticeably cracked; replaced and re-ran; Nilo said new photos look good.&nbsp; Discussion with Doug on a different material that would not crack with our reagents.
* Mack;&nbsp; flush puck may still be stuck as it hasn't been used.&nbsp; will check after lunch
* Cheri busy ordering parts for other two cores.
* One cart has a flat tire.

h3. MFB

* Jose currently busy, but will be available in 1 week to do wiring harnesses; he'll build 2, send rest out for manufacture.
* Parts ordered for serial connector to core; should be here Monday/Tuesday
* 2nd grill:&nbsp; Addie writing scripts for PCR and SPE
* Encoder/Dwarf;&nbsp; Addie had interesting problem where MFB froze, but after shutting several open windows, control was regained....&nbsp; Dwarf losing thje encoder count has not occurred again, but unclear why.&nbsp; Rebooting fixed.
* Chris P. has run plasmids on NEO MFB, and now negatives are coming up positive.&nbsp; She still needs to do a full-decon, and may require longer hot bleach times.
* Chris P. is setting up for a BAC superphase, to be run with debugging on.&nbsp; Much preparation, so the actual run may not begin until Monday.

h3. Software

* &nbsp;Xlinx issue; Brent and Scott working in bldg B to try and understand how encoder counts are being lost/dropped
* Jim (and possibly Roman) are starting a Ruby commenting project.&nbsp; Ultimate goal is to write a 'users manual' for the ESP.

h3. DWSM


h6. +Sphere+

* Wah Chang has been notified of potential repair and is looking into their policy.&nbsp; Regardless, we will ship the sphere back to them for dye testing to make sure there are no other surface voids that HIP could not eliminate, but we can't see.
* Tapemation should be finished with machining this week.&nbsp; Doug to check.
* Min-K delivery has moved from 6 weeks to 11 weeks (ordered 9-22-08); Scott has called and waiting to hear compny update.
* Pressure test facility information (from Mark Brown):
** Hi Mark,

Given the size of your housing it will fit in our 72" dia pressure
vessel which is rated for 5,400 psi. It was rated for 5,500 psi but the
Navy Hyperbaric System Certification people said we had to have put a
relief valve on the vessel that is rated at the max working pressure
(5,500 psi). To be on the safe side, we only go to 5,400 psi.

The daily rate is still $1,800 until Jan. 1, 2009 then it will be
$2,100.00. December is open except for the week of the 8th and from the
25th till Jan. 5th.

If you need more information then please give me a call or Fernando
Ruiz. (805) 982-2054

Thanks,
Mark

Mark Wells
NFESC, Deep Ocean Simulation Facility
1100 23rd Ave
Port Hueneme, CA 93043

v (805) 982-1531
c (805) 766-8389
f (805) 982-1938

h6. +DWSM+

* &nbsp;Doug has sent up warning flare that our first DWSM deployment is rapidly approaching (Feb. 23), and we should start upper level programming of DWSM in parallel with the lower level testing that can currently occur.&nbsp; Brent/Wayne/Scott working on getting both upper and lower level testing up and running.
* Many parts to be ordered for elevator.
* Doug wants first deployment to be test of elevator with surrogate sphere (weights) to test deployment/recovery procedures.&nbsp; The next deployment we should have sphere pressure-tested and can add to the elevator.

h3. GUI Development

* &nbsp;Chris P. working with Kevin to better incorporate data processing within Alfresco

h3. Other Items:

* &nbsp;Thanks to Scott for an excellent job at cleaning the high-bay post-deployment and also the Bldg B clean-up.
{note:title=Remember}Please remember to use ESD straps in the bldg A lab, as most of its chairs and countertops have failed ESD testing.&nbsp; Dick Littlefield looking into seat-covers that are ESD compliant.
{note}]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">7405588</id>
<property name="body"><![CDATA[Present: Scott, Doug, Addie, Kevin, Jim, Cheri, Brent, Wayne

Absent:&nbsp; Chris S (in China)

h3. Deployment Update

* &nbsp;

h3. Machine Builds

* &nbsp;Moe now has GG's harmonic drive part of the hand.&nbsp; Cheri noticed that GG's lower hand is sticky; could be slider, could be bad motor.
* Bruce leak.&nbsp; Found that o-rings in processing clamp were noticeably cracked; replaced and re-ran; Nilo said new photos look good.&nbsp; Discussion with Doug on a different material that would not crack with our reagents.
* Mack;&nbsp; flush puck may still be stuck as it hasn't been used.&nbsp; will check after lunch
* Cheri busy ordering parts for other two cores.
* One cart has a flat tire.

h3. MFB

* Jose currently busy, but will be available in 1 week to do wiring harnesses; he'll build 2, send rest out for manufacture.
* Parts ordered for serial connector to core; should be here Monday/Tuesday
* 2nd grill:&nbsp; Addie writing scripts for PCR and SPE
* Encoder/Dwarf;&nbsp; Addie had interesting problem where MFB froze, but after shutting several open windows, control was regained....&nbsp; Dwarf losing thje encoder count has not occurred again, but unclear why.&nbsp; Rebooting fixed.
* Chris P. has run plasmids on NEO MFB, and now negatives are coming up positive.&nbsp; She still needs to do a full-decon, and may require longer hot bleach times.
* Chris P. is setting up for a BAC superphase, to be run with debugging on.&nbsp; Much preparation, so the actual run may not begin until Monday.

h3. Software

* &nbsp;Xlinx issue; Brent and Scott working in bldg B to try and understand how encoder counts are being lost/dropped
* Jim (and possibly Roman) are starting a Ruby commenting project.&nbsp; Ultimate goal is to write a 'users manual' for the ESP.

h3. DWSM


h6. +Sphere+

* Wah Chang has been notified of potential repair and is looking into their policy.&nbsp; Regardless, we will ship the sphere back to them for dye testing to make sure there are no other surface voids that HIP could not eliminate, but we can't see.
* Tapemation should be finished with machining this week.&nbsp; Doug to check.
* Min-K delivery has moved from 6 weeks to 11 weeks (ordered 9-22-08); Scott has called and waiting to hear compny update.
* Pressure test facility information (from Mark Brown):
{color:blue}** Hi Mark,

Given the size of your housing it will fit in our 72" dia pressure
vessel which is rated for 5,400 psi. It was rated for 5,500 psi but the
Navy Hyperbaric System Certification people said we had to have put a
relief valve on the vessel that is rated at the max working pressure
(5,500 psi). To be on the safe side, we only go to 5,400 psi.

The daily rate is still $1,800 until Jan. 1, 2009 then it will be
$2,100.00. December is open except for the week of the 8th and from the
25th till Jan. 5th.

If you need more information then please give me a call or Fernando
Ruiz. (805) 982-2054

Thanks,
Mark

Mark Wells
NFESC, Deep Ocean Simulation Facility
1100 23rd Ave
Port Hueneme, CA 93043

v (805) 982-1531
c (805) 766-8389
f (805) 982-1938 {color}

h6. +DWSM+

* &nbsp;Doug has sent up warning flare that our first DWSM deployment is rapidly approaching (Feb. 23), and we should start upper level programming of DWSM in parallel with the lower level testing that can currently occur.&nbsp; Brent/Wayne/Scott working on getting both upper and lower level testing up and running.
* Many parts to be ordered for elevator.
* Doug wants first deployment to be test of elevator with surrogate sphere (weights) to test deployment/recovery procedures.&nbsp; The next deployment we should have sphere pressure-tested and can add to the elevator.

h3. GUI Development

* &nbsp;Chris P. working with Kevin to better incorporate data processing within Alfresco

h3. Other Items:

* &nbsp;Thanks to Scott for an excellent job at cleaning the high-bay post-deployment and also the Bldg B clean-up.
{note:title=Remember}Please remember to use ESD straps in the bldg A lab, as most of its chairs and countertops have failed ESD testing.&nbsp; Dick Littlefield looking into seat-covers that are ESD compliant.
{note}]]></property>
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<id name="id">7405578</id>
<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]
# [04Sep2008]
# [11Sep2008]
# [18Sep2008]
# [25Sep2008]
# [02Oct2008] (Pre-deployment discussions)
# [09Oct2008] (the day after deployment....)
# [16Oct2008]
# [23Oct2008]
# [30Oct2008]]]></property>
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</property>
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<id name="id">7405581</id>
<property name="body"><![CDATA[Present: Chris S., Scott, Kevin, Jim, Doug, Wayne, Addie

Absent: Cheri, Brent

h3. Deployment Update

* &nbsp;

h3. Machine Builds

* &nbsp;

h3. MFB

* &nbsp;

h3. Software

* &nbsp;

h3. DWSM


h6. +Sphere+

* &nbsp;

h6. +DWSM+

* &nbsp;

h3. GUI Development

* &nbsp;

h3. Other Items:

* &nbsp;]]></property>
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<property name="body"><![CDATA[Present:


Absent:


h3. Deployment Update

* &nbsp;

h3. Machine Builds

* &nbsp;

h3. MFB

* &nbsp;

h3. Software

* &nbsp;

h3. DWSM


h6. +Sphere+

* &nbsp;

h6. +DWSM+

* &nbsp;

h3. GUI Development

* &nbsp;

h3. Other Items:

* &nbsp;]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">7405585</id>
<property name="body"><![CDATA[Present: Scott, Doug, Addie, Kevin, Jim, Cheri, Brent, Wayne

Absent:&nbsp; Chris S (in China)

h3. Deployment Update

* &nbsp;

h3. Machine Builds

* &nbsp;Moe now has GG's harmonic drive part of the hand.&nbsp; Cheri noticed that GG's lower hand is sticky; could be slider, could be bad motor.
* Bruce leak.&nbsp; Found that o-rings in processing clamp were noticeably cracked; replaced and re-ran; Nilo said new photos look good.&nbsp; Discussion with Doug on a different material that would not crack with our reagents.
* Mack;&nbsp; flush puck may still be stuck as it hasn't been used.&nbsp; will check after lunch
* Cheri busy ordering parts for other two cores.
* One cart has a flat tire.

h3. MFB

* Jose currently busy, but will be available in 1 week to do wiring harnesses; he'll build 2, send rest out for manufacture.
* Parts ordered for serial connector to core; should be here Monday/Tuesday
* 2nd grill:&nbsp; Addie writing scripts for PCR and SPE
* Encoder/Dwarf;&nbsp; Addie had interesting problem where MFB froze, but after shutting several open windows, control was regained....&nbsp; Dwarf losing thje encoder count has not occurred again, but unclear why.&nbsp; Rebooting fixed.
* Chris P. has run plasmids on NEO MFB, and now negatives are coming up positive.&nbsp; She still needs to do a full-decon, and may require longer hot bleach times.
* Chris P. is setting up for a BAC superphase, to be run with debugging on.&nbsp; Much preparation, so the actual run may not begin until Monday.

h3. Software

* &nbsp;Xlinx issue; Brent and Scott

h3. DWSM


h6. +Sphere+

* Wah Chang has been notified of potential repair and is looking into their policy.&nbsp; Regardless, we will ship the sphere back to them for dye testing to make sure there are no other surface voids that HIP could not eliminate, but we can't see.
* Tapemation should be finished with machining this week.&nbsp; Doug to check.
* Min-K delivery has moved from 6 weeks to 11 weeks (ordered 9-22-08); Scott has called and waiting to hear compny update.
* Pressure test facility information (from Mark Brown):
** Hi Mark,

Given the size of your housing it will fit in our 72" dia pressure
vessel which is rated for 5,400 psi. It was rated for 5,500 psi but the
Navy Hyperbaric System Certification people said we had to have put a
relief valve on the vessel that is rated at the max working pressure
(5,500 psi). To be on the safe side, we only go to 5,400 psi.

The daily rate is still $1,800 until Jan. 1, 2009 then it will be
$2,100.00. December is open except for the week of the 8th and from the
25th till Jan. 5th.

If you need more information then please give me a call or Fernando
Ruiz. (805) 982-2054

Thanks,
Mark

Mark Wells
NFESC, Deep Ocean Simulation Facility
1100 23rd Ave
Port Hueneme, CA 93043

v (805) 982-1531
c (805) 766-8389
f (805) 982-1938

h6. +DWSM+

* &nbsp;Doug has sent up warning flare that our first DWSM deployment is rapidly approaching (Feb. 23), and we should start upper level programming of DWSM in parallel with the lower level testing that can currently occur.&nbsp; Brent/Wayne/Scott working on getting both upper and lower level testing up and running.
* Many parts to be ordered for elevator.
* Doug wants first deployment to be test of elevator with surrogate sphere (weights) to test deployment/recovery procedures.&nbsp; The next deployment we should have sphere pressure-tested and can add to the elevator.

h3. GUI Development

* &nbsp;

h3. Other Items:

* &nbsp;Thanks to Scott for an excellent job at cleaning the high-bay post-deployment and also the Bldg B clean-up.
* Please remember to use ESD straps in the bldg A lab, as most of its chairs and countertops have failed ESD testing.&nbsp; Dick Littlefield looking into seat-covers that are ESD compliant.]]></property>
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<id name="id">19073514</id>
<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.

June 26 - continues to run, but lost internet access due to an unknown networking error.

h3. {color:#ff00ff}So. California Deployment of ESP-Gordon / NEO{color}

Aug 30 \-\- Haul instrument and gear in trailer and MBARI van to deploy on OCSD R/V Nerissa.  Calm seas, hot weather, instrument in \~10:30am.  Gordon w/PCR, CTD, ISUS, cell-phone modem (T-Mobile).  Sewage diversion to begin Sep 11, 2012.]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19073516</id>
<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.

June 26 - continues to run, but lost internet access due to an unknown networking error.

h3. {color:#ff00ff}So. California Deployment of ESP-Gordon / NEO{color}

Aug 30 \-\- Haul instrument and gear in trailer and MBARI van to deploy on OCSD R/V Nerissa.  Calm seas, hot weather, instrument in \~10:30am.  Gordon w/PCR, CTD, ISUS, cell-phone modem (T-Mobile).  Sewage diversion to begin Sep 11, 2012.

h3. {color:#ff00ff}Fall CANON--Drifter with ESP-Moe / Moe{color}

WF leaves MBARI Sept 11.&nbsp; Moe with PCR, ISUS, CTD, PAR, and buoy has downward ADCP.&nbsp; Roman and Julie R. on ship. ]]></property>
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<id name="id">19073517</id>
<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.

June 26 - continues to run, but lost internet access due to an unknown networking error.

h3. {color:#ff00ff}So. California Deployment of ESP-Gordon / NEO{color}

Aug 30 \-\- Haul instrument and gear in trailer and MBARI van to deploy on OCSD R/V Nerissa.  Calm seas, hot weather, instrument in \~10:30am.  Gordon w/PCR, CTD, ISUS, cell-phone modem (T-Mobile).  Sewage diversion to begin Sep 11, 2012.

h3. {color:#ff00ff}Fall CANON--Drifter with ESP-Moe / Moe{color}

WF leaves MBARI Sept 10.&nbsp; Moe with PCR, ISUS, CTD, PAR, and buoy has downward ADCP.&nbsp; Roman and Julie R. on ship.

Moe went into water Sep 11. First phase slated for 6pm.]]></property>
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<property name="body"><![CDATA[This space serves as a repository of ESP development ideas and decisions.]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19073481</id>
<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.

June 26 - continues to run, but lost internet access due to an unknown networking error. 

h3. {color:#ff00ff}So. California Deployment of ESP-Gordon{color}

Aug 30 \-\- Haul instrument and gear in trailer and MBARI van to deploy on OCSD R/V Nerissa.  Calm seas, hot weather, instrument in ~10:30am.  Gordon w/PCR, CTD, ISUS, cell-phone modem (T-Mobile).  Sewage diversion to begin Sep 11, 2012.]]></property>
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<id name="id">19073480</id>
<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.

June 26 - continues to run, but lost internet access due to an unknown networking error. ]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]
# [May 20]
# [May 27]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 18 Feb 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [MFB-PCR distribution list] as of 05Apr2010]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

&nbsp;[Planning Documents for JdeFuca cruise, July 2011] ]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24]]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Scott, Brent, Doug, Jim, Gene

Absent:&nbsp; Chris S., Cheri, Addie, Wayne

h3. Machine Builds


h3. MFB


h3. Drifter

* Pre-Flyer cruise dive days on the Zephyr have been pushed back to May 26 and May 27
* Gene will be in Test Tank Monday/Tuesday
* Ordering radar reflector.&nbsp; Have blinky light.&nbsp; PPP is running via wire.&nbsp; Scott will set-up Freewave's
* If time, will pull Iridium off an existing surface mooring and mount on Drifter.

h3. Software

* Brent's been working on HP pump.&nbsp; It seems to run either full on or off.&nbsp; Difficult to run it at other than 2000rpm.&nbsp; He has a was to work servo control with this constraint.
* Next is to characterize the differential pressure sensors then
* run sample fluid through the core loop
* Noticed that TSV seems to get off by 7-9 counts when you power cycle. Scott will watch while they try and re-create.
* Discussion about making the laptop on the boat a 'slave' to the shorestation, so missions can be started right on the boat (boat laptop\--> shore station-\->ESP buoy) instead of having to rely on someone on the shore.

h3. Deep ESP


h6.

* Will talk to Science about needs for a metal wand to withstand high temperatures at Axial.&nbsp; Otherwise, with current design, the end of the 'wand' is actually a solenoid valve.
* Doug showed valve design to Brent and explained function.
* Must get Science buy-in about wand idea, but in the meantime we will push forward with this design.

h3. GUI


h3. Deployment Issues

* Two potential sites to visit in June:
* \#1.&nbsp; 2900m \[36.61N, 122.44W\].&nbsp; Flat, open, clear water.&nbsp; Nearby clam-field.
* \#2.&nbsp; 1800m \[36.71N, 122.1W\].&nbsp; Flat, poorer visibility.&nbsp; very old whale-fall.
* Much discussion of which site.&nbsp; Consensus was that August cruise is most critical (depths of 1400-1600m), thus site #2 would provide adequate testing for August without undue risk.&nbsp;&nbsp;
* A very rough deployment schedule was discussed.&nbsp; Leave MBARI @ 11am on Friday, June 5, return Tuesday, June 9.&nbsp; Chris and I will meet with ship crew 10am (Tank View) Tuesday to discuss.
* 4K ISUS mtg Tuesday @ 11--Tank View.&nbsp; Will meet with Luke, John R., and science.

h3. Other Items:]]></property>
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<property name="body"><![CDATA[h2. Engineering weekly meeting (Dec 20, 2007)

# Software situation
*2 bugs*

## Continuation
## Dead Parents

Enough runs yet?# NEO completes 5 runs continuously, should we run 5 more?&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;
Concern is we may run low on reagents.&nbsp; No, hand over to science now that Brent has handle on where two bugs are.]]></property>
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<property name="body"><![CDATA[h2. Engineering weekly meeting (Dec 20, 2007)

*Tech Transfer*

•&nbsp;&nbsp; &nbsp;Light seals changed?
•&nbsp;&nbsp; &nbsp;Status of slow-running intake
•&nbsp;&nbsp; &nbsp;Status of manipulator hands.&nbsp; How many needed?&nbsp; How many made?&nbsp; Where are those installed?&nbsp; Waiting on any parts for hand?
•&nbsp;&nbsp; &nbsp;Status of motors and motor-mounts?
•&nbsp;&nbsp; &nbsp;Any questions about published timeline?
•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?
•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?
•&nbsp;&nbsp; &nbsp;Discussion of IP tech transfer w/ LLNL?

*MFB*
•&nbsp;&nbsp; &nbsp;What will be MFB status as of 12-21-07?
•&nbsp;&nbsp; &nbsp;When will all parts be in for 2nd MFB?
•&nbsp;&nbsp; &nbsp;What is left in extraction protocol?

*Software*
Brent gone until Jan 2nd.

*Sphere and 4K DWSMS*
•&nbsp;&nbsp; &nbsp;Sphere ordered by Jon Erikson on Dec 13, 2007.

Funny Money Expenditures
•&nbsp;&nbsp; &nbsp;Currently getting quote on 3 cans/endcaps; do we need for current year?
•&nbsp;&nbsp; &nbsp;Pucks?
•&nbsp;&nbsp; &nbsp;Other End-of-year expenses?

*Issues from Doug:*

•&nbsp;&nbsp; &nbsp;Serial numbering of pucks.
•&nbsp;&nbsp; &nbsp;Image reflections on puck.&nbsp; Still and issue?
•&nbsp;&nbsp; &nbsp;Concern on cleanliness of SSfittings off deep chamber
•&nbsp;&nbsp; &nbsp;Pressure pots; rust source?
•&nbsp;&nbsp; &nbsp;Battery/power issues for spring deployments
*4K stuff:*
1. I have lower, more reasonable quotes for the sample chambers, but
they're trepanning solid stock so it's still pricey. It is something
that we could do or have El Camino do instead. I'll need to touch base
with Mike to see if it's worth while. Maybe a competitive quote from El
Cam.
2. We don't have a lot of time (20 weeks lead time on these) but I'm
looking into a steel housing to proof the system before. End caps and
penetrators would still be TI, but $40k would buy a lot.
3. I've made some small (but measureable with an interferometer)
progress on the 1k article.



*Timeline (from Confluence):*
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.12|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.2%10_12_2007%202%2011_19_2007.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram12-19-07.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.12|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.2%2010_12_2007%202%2011_19_2007.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram12-19-07.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h2. Meeting minutes stored in the projectlibrary:&nbsp;

# [Meeting Notes from June 7, 2007|http://oceana.shore.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc]
\\

h2. Meeting minutes stored within Confluence:

# [08nov2007]
# [15Nov2007]
# [29Nov2007]
# [06Dec2007]]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.12|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.1%202%2011_19_2007.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram11-27-07.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.12|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.1%202%2011_19_2007.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram12-19-07.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.12|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.2 10_12_2007%202%2011_19_2007.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram12-19-07.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]
]]></property>
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<property name="body"><![CDATA[h2. Outline of instrument plan for Jan-Jun, 2008

\\
# Cold Test Bruce with his new hand (2 weeks; Dec 31-->Jan 15)
Revalve Mack to new motors and mounts

# Cold test Mack w/ his new valves/hand (2 weeks; Jan 15-->Jan 29)
Revalve Bruce and Neo

\#]]></property>
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<property name="body"><![CDATA[# 2008 Q1/Q2]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">2163080</id>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/fluid%20worksheet%20MFB%2014-MAR-07.pdf]
# [Engineering Timeline Q1/Q2 2008]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]

h2. Science]]></property>
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<property name="body"><![CDATA[Subject: Machining 4k sphere
Date: Wed, 5 Dec 2007 08:25:41 \-0800
Thread-Topic: Machining 4k sphere
Thread-Index: Acg3W3pDdPq8Hs8jRtKanjDmUGXOrA==
From: "Brown, Mark" <mob@mbari.org>
To: "Birch, James" <jbirch@mbari.org>,
&nbsp;&nbsp;&nbsp; "Scholin, Chris" <scholin@mbari.org>

Jim & Chris\-
Just to keep you up to date\-
For machining the large 4k sphere's we have one quote from our local vendor (Tapemation) that came in approx. $40,000. We had another vendor in Oregon just get back to us with a "no quote" and they said this was outside of their comfort zoneL
&nbsp;
I have a call into our casting vendor Wah Chang asking about who they might have dealt with for a large casting such as this and I will let you know what I find out.
\-Mark
Mark Brown
Support Engineering&nbsp;Group Leader
MBARI: <http://www.mbari.org>www.mbari.org
ph: 831 775 1939
fx: 831 775 1615]]></property>
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<property name="body"><![CDATA[h2. ESP weekly meeting (Dec 20, 2007)

*Present:* Cheri, Scott, Chris P., Jim, Addie, Chris S.

*Tech Transfer*

&nbsp; &nbsp;Light seals changed?
{color:#3300ff}yes{color}

•&nbsp;&nbsp; &nbsp;Status of slow-running intake
{color:#3300ff}Need to check this out with GG.&nbsp; Science may not be needing it; Chris will Check. Scotts concerned that lower pressure sensor has changed its calibration by 50%.&nbsp; Would like to remove it to look for fouling.&nbsp; Chris mentioned 'blowing-up' a fragile bug because of larger pressure differential; sensor could be culprit.{color}

{color:#ff0000}ACTION:{color} is science finished with GG (Chris S)&nbsp;

{color:#ff0000}ACTION:{color} remove GG lower pressure sensor and examine (Scott)&nbsp;

•&nbsp;&nbsp; &nbsp;Status of manipulator hands.&nbsp; How many needed?&nbsp; How many made?&nbsp; Where are those installed?&nbsp; Waiting on any parts for hand?
{color:#3300ff}Still futzing with first redesigned hand.&nbsp; Very touchy assembly. Have 3 built but have found a problem with cam motor-mount.{color}

{color:#ff0000}ACTION:&nbsp;{color} meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)

•&nbsp;&nbsp; &nbsp;Status of motors and motor-mounts?
{color:#3300ff}Have all motors.&nbsp; Have all mounts.&nbsp; Mike is modifying encoder gears.{color}

•&nbsp;&nbsp; &nbsp;Any questions about published timeline?
{color:#3300ff}Will be using piezo-arrays for all these testings.&nbsp;{color}

{color:#ff0000}ACTION:{color}&nbsp; Need a Gantt chart of instrument usage (Jim)

•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?
{color:#3300ff}they sent a drawing of what they planned on doing (2 weeks ago?).&nbsp; Scott replied; do it.&nbsp; Haven't heard from them yet.{color}

{color:#ff0000}ACTION:{color} call and find out where they are (Scott)

•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?

{color:#ff0000}ACTION:{color} Must check with Jose.&nbsp; He's adding up inventory.&nbsp; Will need enough for 2 cores and 8 MFB and spares (at least 1 full core and enough spares for 8 MFB's\[3 dwarves, 2 R's\]).&nbsp; Tally up, look at production run, and scale up for best economy.&nbsp; Will place order early January. (Scott)

•&nbsp;&nbsp; &nbsp;Discussion of IP tech transfer w/ LLNL?
{color:#3300ff}Update:&nbsp; we have written agreement with LLNL that UH, WHOI, is aproved.&nbsp; Foreign use is unknown and Patrice is looking into it.&nbsp; Valve design TBD{color}

{color:#ff0000}ACTION:{color}&nbsp; Clarify IP on valve design (Chris)&nbsp;

*MFB*
•&nbsp;&nbsp; &nbsp;What will be MFB status as of 12-21-07?
{color:#3300ff}Solid phase extraction working well.&nbsp; Running through lysate coil on AIV.&nbsp; Slug still shows a gradient, first 100ul good, second 100ul (over column) has high concentration.&nbsp; Going to try just pushing 100ul through.&nbsp; Unable to find mixing chambers, so will only take 100, push to and fro a few times and it'll be mixed.&nbsp; Chris P thinks it may be TOO concentrated, bench rocovery is 12-25ug, and extrction is 25ug minimum.&nbsp; Still tweaking this.&nbsp; This will be January focus.&nbsp; Standardize the protocol for this.{color}

•&nbsp;&nbsp; &nbsp;When will all parts be in for 2nd MFB?
{color:#3300ff}All parts are in except MAXON motors.&nbsp;&nbsp; Cheri ordered 33 total, 27 for her and 6 for Addie (who has used 4, 2 are around MBARI) and needs to order 6 more.&nbsp; Cheri will use 24 w/ 1 spare apiece.&nbsp;{color}

{color:#ff0000}ACTION:{color}{color:#000000}&nbsp; place order with MAXON for MFB spares (Addie){color}

•&nbsp;&nbsp; &nbsp;What is left in extraction protocol?&nbsp; {color:#3300ff}Finalization of protocols will be early January.{color}

{color:#3300ff}{*}Chris Scholin hosting CMORE workshop Jan. 14-17 (35 people from OR, HI, WHOI) to define functional requirements for our and other partners CMORE work.*{color}{color:#3300ff}&nbsp; Suggests that we clean up MFB and put on cart, and do a demo run.&nbsp; Get rid of power board and zip tie things and tubing wraps, etc.{color}

{color:#3300ff}Dscussion about LLNL, when they will get a new block to us.&nbsp; If we get the driver block, we should have it out for display.{color}

{color:#3300ff}Discussion about PSV valve.&nbsp; Addie will add the PSV valve.&nbsp; Discussion about connections b/w core and MFB.{color}

{color:#ff0000}ACTION:{color} Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addie will figure out how to connect ports 3, 5, 6 with no bubbles. (Addie)

{color:#ff0000}ACTION:{color}&nbsp; Lubricating syringe.&nbsp; Must be 'upside-down' to prime with no air bubbles.&nbsp; But then could rotate 180 so it retains lubricant. Investigate remounting this right-side up after priming (Addie & Scott)

{color:#ff0000}ACTION:{color}&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (Scott will email)

*Software*
Brent gone until Jan 2nd.

*Sphere and 4K DWSMS*
•&nbsp;&nbsp; &nbsp;Sphere ordered by Jon Erikson on Dec 13, 2007.

*Funny Money Expenditures*
•&nbsp;&nbsp; &nbsp;Currently getting quote on 3 cans/endcaps; do we need for current year?

{color:#3300ff}We have two complete surface moorings (although one can is a 'spare').&nbsp; Will turn off mooring hardware PO from 2006.{color}
•&nbsp;&nbsp; &nbsp;Pucks?

{color:#3300ff}Mike will have a quote tomorrow.{color}
{color:#3300ff}big expenses should go through Chris S for spreading charges among accounts.{color}

*Issues from Doug:*

•&nbsp;&nbsp; &nbsp;Serial numbering of pucks.

{color:#ff0000}ACTION:{color} Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott)

•&nbsp;&nbsp; &nbsp;Image reflections on puck.&nbsp; Still and issue?
{color:#3300ff}no{color}
•&nbsp;&nbsp; &nbsp;Concern on cleanliness of SSfittings off deep chamber
{color:#3300ff}We are only using electrical connctors, not fluid connectors. May have to order fluid fittings for 'box test'.{color}

{color:#ff0000}ACTION:{color} look into need for new fluid fittings and order if necessary (Cheri)

•&nbsp;&nbsp; &nbsp;Pressure pots; rust source?
{color:#3300ff}Will clean and should be okay.{color}

{color:#ff0000}ACTION:{color} Cheri to get pressure pot sizes to figure box structure. (Cheri)

{color:#ff0000}ACTION:&nbsp;{color} Pressure posts. We want this inventory: 2 fives, 2 tens, 2 threes.&nbsp; Must order enough to reach this inventory (Chris P)

•&nbsp;&nbsp; &nbsp;Battery/power issues for spring deployments
{color:#3300ff}stick with alkaline.&nbsp; Do we need more boxes?&nbsp; Need 4 boxes initially.&nbsp; Not working on low power issues.&nbsp; Must order minimum of 1 box of batteries in early 2008.{color}

*4K stuff:*
1. I have lower, more reasonable quotes for the sample chambers, but
they're trepanning solid stock so it's still pricey. It is something
that we could do or have El Camino do instead. I'll need to touch base
with Mike to see if it's worth while. Maybe a competitive quote from El
Cam.
2. We don't have a lot of time (20 weeks lead time on these) but I'm
looking into a steel housing to proof the system before. End caps and
penetrators would still be TI, but $40k would buy a lot.
3. I've made some small (but measureable with an interferometer)
progress on the 1k article.

*Timeline (This schedule is its own page in Confluence):*
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.

{color:#3300ff}Cold testing of Bruce is really just 'hand' cold-testing.&nbsp; Valving and tubing tests commence with Ma{color}ck.

*Items Pending:*

battery box
stedim bags for aqualung&nbsp;
Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp;]]></property>
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<property name="body"><![CDATA[h2. Quotes

* Sphere casting [(Wah Chang)|^Wah Chang quote MBARI 60200 11-14 C5.pdf]
* Machining
** [Tapemation|^Tapemation quote MBARI 4K Hemi.doc]
** Hanard Machine (sent for quote 11-15-07)]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation. Done in three stages
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{jiraissues:https://oceana.mbari.org/jira/sr/jira.issueviews:searchrequest-xml/temp/SearchRequest.xml?&pid=10050&status=1&status=3&status=4&component=10082&sorter/field=issuekey&sorter/order=DESC&sorter/field=priority&sorter/order=DESC&tempMax=1000|anonymous=true}
{panel}


]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.12|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.2%2010_12_2007.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram12-19-07.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h2. Engineering weekly meeting (Dec 20, 2007)

*Present:* Cheri, Scott, Chris P., Jim, Addie, Chris S.

*Tech Transfer*

&nbsp; &nbsp;Light seals changed?
{color:#3300ff}yes{color}

•&nbsp;&nbsp; &nbsp;Status of slow-running intake
{color:#3300ff}Need to check this out with GG.&nbsp; Science may not be needing it; Chris will Check. Scotts concerned that lower pressure sensor has changed its calibration by 50%.&nbsp; Would like to remove it to look for fouling.&nbsp; Chris mentioned 'blowing-up' a fragile bug because of larger pressure differential; sensor could be culprit.{color}

{color:#ff0000}ACTION:{color} is science finished with GG (Chris S)&nbsp;

{color:#ff0000}ACTION:{color} remove GG lower pressure sensor and examine (Scott)&nbsp;

•&nbsp;&nbsp; &nbsp;Status of manipulator hands.&nbsp; How many needed?&nbsp; How many made?&nbsp; Where are those installed?&nbsp; Waiting on any parts for hand?
{color:#3300ff}Still futzing with first redesigned hand.&nbsp; Very touchy assembly. Have 3 built but have found a problem with cam motor-mount.{color}

{color:#ff0000}ACTION:&nbsp;{color} meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)

•&nbsp;&nbsp; &nbsp;Status of motors and motor-mounts?
{color:#3300ff}Have all motors.&nbsp; Have all mounts.&nbsp; Mike is modifying encoder gears.{color}

•&nbsp;&nbsp; &nbsp;Any questions about published timeline?
{color:#3300ff}Will be using piezo-arrays for all these testings.&nbsp;{color}

{color:#ff0000}ACTION:{color}&nbsp; Need a Gantt chart of instrument usage (Jim)

•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?
{color:#3300ff}they sent a drawing of what they planned on doing (2 weeks ago?).&nbsp; Scott replied; do it.&nbsp; Haven't heard from them yet.{color}

{color:#ff0000}ACTION:{color} call and find out where they are (Scott)

•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?

{color:#ff0000}ACTION:{color} Must check with Jose.&nbsp; He's adding up inventory.&nbsp; Will need enough for 2 cores and 8 MFB and spares (at least 1 full core and enough spares for 8 MFB's\[3 dwarves, 2 R's\]).&nbsp; Tally up, look at production run, and scale up for best economy.&nbsp; Will place order early January. (Scott)

•&nbsp;&nbsp; &nbsp;Discussion of IP tech transfer w/ LLNL?
{color:#3300ff}Update:&nbsp; we have written agreement with LLNL that UH, WHOI, is aproved.&nbsp; Foreign use is unknown and Patrice is looking into it.&nbsp; Valve design TBD{color}

{color:#ff0000}ACTION:{color}&nbsp; Clarify IP on valve design (Chris)&nbsp;

*MFB*
•&nbsp;&nbsp; &nbsp;What will be MFB status as of 12-21-07?
{color:#3300ff}Solid phase extraction working well.&nbsp; Running through lysate coil on AIV.&nbsp; Slug still shows a gradient, first 100ul good, second 100ul (over column) has high concentration.&nbsp; Going to try just pushing 100ul through.&nbsp; Unable to find mixing chambers, so will only take 100, push to and fro a few times and it'll be mixed.&nbsp; Chris P thinks it may be TOO concentrated, bench rocovery is 12-25ug, and extrction is 25ug minimum.&nbsp; Still tweaking this.&nbsp; This will be January focus.&nbsp; Standardize the protocol for this.{color}

•&nbsp;&nbsp; &nbsp;When will all parts be in for 2nd MFB?
{color:#3300ff}All parts are in except MAXON motors.&nbsp;&nbsp; Cheri ordered 33 total, 27 for her and 6 for Addie (who has used 4, 2 are around MBARI) and needs to order 6 more.&nbsp; Cheri will use 24 w/ 1 spare apiece.&nbsp;{color}

{color:#ff0000}ACTION:{color}{color:#000000}&nbsp; place order with MAXON for MFB spares (Addie){color}

•&nbsp;&nbsp; &nbsp;What is left in extraction protocol?&nbsp; {color:#3300ff}Finalization of protocols will be early January.{color}

{color:#3300ff}Chris Scholin hosting CMORE workshop Jan. 14-17 (35 people from OR, HI, WHOI) to define functional requirements for our and other partners CMORE work.&nbsp; Suggests that we clean up MFB and put on cart, and do a demo run.&nbsp; Get rid of power board and zip tie things and tubing wraps, etc.{color}

{color:#3300ff}Dscussion about LLNL, when they will get a new block to us.&nbsp; If we get the driver block, we should have it out for display.{color}

{color:#3300ff}Discussion about PSV valve.&nbsp; Addie will add the PSV valve.&nbsp; Discussion about connections b/w core and MFB.{color}

{color:#ff0000}ACTION:{color} Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addie will figure out how to connect ports 3, 5, 6 with no bubbles. (Addie)

{color:#ff0000}ACTION:{color}&nbsp; Lubricating syringe.&nbsp; Must be 'upside-down' to prime with no air bubbles.&nbsp; But then could rotate 180 so it retains lubricant. Investigate remounting this right-side up after priming (Addie & Scott)

{color:#ff0000}ACTION:{color}&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (Scott will email)

*Software*
Brent gone until Jan 2nd.

*Sphere and 4K DWSMS*
•&nbsp;&nbsp; &nbsp;Sphere ordered by Jon Erikson on Dec 13, 2007.

*Funny Money Expenditures*
•&nbsp;&nbsp; &nbsp;Currently getting quote on 3 cans/endcaps; do we need for current year?

{color:#3300ff}We have two complete surface moorings (although one can is a 'spare').&nbsp; Will turn off mooring hardware PO from 2006.{color}
•&nbsp;&nbsp; &nbsp;Pucks?
{color:#3300ff}big expenses should go through Chris S for spreading charges among accounts.{color}
{color:#3300ff}Mike will have a quote tomorrow.{color}

*Issues from Doug:*

•&nbsp;&nbsp; &nbsp;Serial numbering of pucks.

{color:#ff0000}ACTION:{color} Collect and inventory all pucks (Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott)

•&nbsp;&nbsp; &nbsp;Image reflections on puck.&nbsp; Still and issue?
{color:#3300ff}no{color}
•&nbsp;&nbsp; &nbsp;Concern on cleanliness of SSfittings off deep chamber
{color:#3300ff}We are only using electrical connctors, not fluid connectors. May have to order fluid fittings for 'box test'.{color}


{color:#ff0000}ACTION:{color} look into need for new fluid fittings and order if necessary (Cheri)

•&nbsp;&nbsp; &nbsp;Pressure pots; rust source?
{color:#3300ff}Will clean and should be okay.{color}

{color:#ff0000}ACTION:{color} Cheri to get pressure pot sizes to figure box structure. (Cheri)

{color:#ff0000}ACTION:&nbsp;{color} Pressure posts. We want this inventory: 2 fives, 2 tens, 2 threes.&nbsp; Must order enough to reach this inventory (Chris P)

•&nbsp;&nbsp; &nbsp;Battery/power issues for spring deployments
{color:#3300ff}stick with alkaline.&nbsp; Do we need more boxes?&nbsp; Need 4 boxes initially.&nbsp; Not working on low power issues.&nbsp; Must order minimum of 1 box of batteries in early 2008.{color}

*4K stuff:*
1. I have lower, more reasonable quotes for the sample chambers, but
they're trepanning solid stock so it's still pricey. It is something
that we could do or have El Camino do instead. I'll need to touch base
with Mike to see if it's worth while. Maybe a competitive quote from El
Cam.
2. We don't have a lot of time (20 weeks lead time on these) but I'm
looking into a steel housing to proof the system before. End caps and
penetrators would still be TI, but $40k would buy a lot.
3. I've made some small (but measureable with an interferometer)
progress on the 1k article.

*Timeline (This schedule is its own page in Confluence):*
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.

{color:#3300ff}Cold testing of Bruce is really just 'hand' cold-testing.&nbsp; Valving and tubing tests commence with Ma{color}ck.


*Items Pending:*

battery box
stedim bags for aqualung&nbsp;
Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp;]]></property>
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<property name="body"><![CDATA[h2. Engineering weekly meeting (Dec 20, 2007)

*Tech Transfer*

•&nbsp;&nbsp; &nbsp;Light seals changed?

yes

•&nbsp;&nbsp; &nbsp;Status of slow-running intake

Need to check this out with GG.&nbsp; Science may not be needing it; Chris will Check. Scotts concerned that lower pressure sensor has changed its calibration by 50%.&nbsp; Would like to remove it to look for fouling.&nbsp; Chris mentioned 'blowing-up' some fragile bug becasue of larger pressure differential

ACTION: is science finished with GG (Chris S)&nbsp;

ACTION: remove GG lower pressure sensor and examine (Scott)&nbsp;

•&nbsp;&nbsp; &nbsp;Status of manipulator hands.&nbsp; How many needed?&nbsp; How many made?&nbsp; Where are those installed?&nbsp; Waiting on any parts for hand?

Still futzing with first redesigned hand.&nbsp; Very touchy assembly. Have 3 built

ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)

•&nbsp;&nbsp; &nbsp;Status of motors and motor-mounts?

Have all motors.&nbsp; Have all mounts.&nbsp; Mike is modifying encoder gears.

•&nbsp;&nbsp; &nbsp;Any questions about published timeline?

Will be using piezo-arrays for all these testing.&nbsp;

ACTION:&nbsp; Need a Gantt chart of instrument usage (Jim)

•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?

they sent a drawing of what they planned on doing (2 weeks ago?).&nbsp; Scott replied; do it.&nbsp; Haven't heard from them yet.

ACTION: call and find out where they are (Scott)

•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?

ACTION: Must check with Jose.&nbsp; He's adding up inventory.&nbsp; Will need enough for 2 cores and 8 MFB and spares (at least 1 full core and enough spares for 8 MFB's\[3 dwarves, 2 R's\]).&nbsp; Tally up, look at production run, and scale up for best economy.&nbsp; Will place order early January.

•&nbsp;&nbsp; &nbsp;Discussion of IP tech transfer w/ LLNL?

Update:&nbsp; we have written agreement with LLNL that UH, WHOI, is aproved.&nbsp; Foreign use is unknown and Patrice is looking into it.&nbsp; Valve design TBD

ACTION:&nbsp; Clarify IP on valve design (Chris)&nbsp;

*MFB*
•&nbsp;&nbsp; &nbsp;What will be MFB status as of 12-21-07?

Solid phase extraction working well.&nbsp; Running through lysate coil on AIV.&nbsp; Slug still shows a gradient, first 100ul good, second 100ul (over column) has high concentration.&nbsp; Going to try just pushing 100ul through.&nbsp; Unable to find mixing chambers, so will only take 100, push to and fro a few times and it'll be mixed.&nbsp; Chris P thinks it may be TOO concentrated, bench rocovery is 12-25ug, and extrction is 25ug minimum.&nbsp; Still tweaking this.&nbsp; This will be January focus.&nbsp; Standardize the protocol for this.
•&nbsp;&nbsp; &nbsp;When will all parts be in for 2nd MFB?

All parts are in except MAXON motors.&nbsp;&nbsp; Cheri ordered 33 total, 27 for her and 6 for Addie (who has used 4, 2 around) and needs to order 6 more(?).&nbsp; Cheri will use 24 w/ 1 spare apiece.&nbsp; ACTION:&nbsp; order from MAXON.

•&nbsp;&nbsp; &nbsp;What is left in extraction protocol?&nbsp; This will all be early January.

Chris Scholin hosting CMORE workshop Jan. 14-17 (35 people from OR, HI, WHOI) to define functional requirements for our and other partners CMORE work.&nbsp; Suggests that we clean up MFB and put on cart, and do a demo run.&nbsp; Get rid of power board and zip tie things and tubing wraps, etc.

Dscussion about LLNL, when they will get a new block to us.&nbsp; If we get the driver block, we should have it out for display.

Discussion about PSV valve.&nbsp; Addie will add the PSV valve.&nbsp; Discussion about connections b/w core and MFB.

ACTION: Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addice will figure out how to connect ports 3, 5, 6 with no bubbles.

ACTION:&nbsp; Lubricating syringe.&nbsp; Must be 'upside-down' to prime with no air bubbles.&nbsp; But then could rotate 180 so it retains lubricant. Investigate remounting this right-side up after priming.

ACTION:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (scot will email)

*Software*
Brent gone until Jan 2nd.

*Sphere and 4K DWSMS*
•&nbsp;&nbsp; &nbsp;Sphere ordered by Jon Erikson on Dec 13, 2007.

Funny Money Expenditures
•&nbsp;&nbsp; &nbsp;Currently getting quote on 3 cans/endcaps; do we need for current year?

We have two complete surface moorings (although one can is a 'spare').&nbsp; Will turn off mooring hardware PO from 2006.
•&nbsp;&nbsp; &nbsp;Pucks?
big expenses should go through Chris S for spreading charges among accounts.


Mike will have a quote tomorrow.


•&nbsp;&nbsp; &nbsp;Other End-of-year expenses?

*Issues from Doug:*

•&nbsp;&nbsp; &nbsp;Serial numbering of pucks.

ACTION: Collect and inventory all pucks (Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott)

•&nbsp;&nbsp; &nbsp;Image reflections on puck.&nbsp; Still and issue?

no
•&nbsp;&nbsp; &nbsp;Concern on cleanliness of SSfittings off deep chamber

We are only using electrical connctors?

ACTION: look into new fluid fittings (Cheri)
\\

•&nbsp;&nbsp; &nbsp;Pressure pots; rust source?

Will clean and should be okay.


ACTION: Cheri to get the sizes to figure box structure. (Cheri)

ACTION:&nbsp; Pressure posts. We want this inventory: 2 fives, 2 tens, 2 threes.&nbsp; Must order enough to reach this inventory (Chris P)

•&nbsp;&nbsp; &nbsp;Battery/power issues for spring deployments

stick with alkaline.&nbsp; Do we need more boxes?&nbsp; Need 4 boxes initially.&nbsp; Not working on low power issues.&nbsp; Must order minimum of 1 box of batteries in early 2008.


*4K stuff:*
1. I have lower, more reasonable quotes for the sample chambers, but
they're trepanning solid stock so it's still pricey. It is something
that we could do or have El Camino do instead. I'll need to touch base
with Mike to see if it's worth while. Maybe a competitive quote from El
Cam.
2. We don't have a lot of time (20 weeks lead time on these) but I'm
looking into a steel housing to proof the system before. End caps and
penetrators would still be TI, but $40k would buy a lot.
3. I've made some small (but measureable with an interferometer)
progress on the 1k article.

*Timeline (from Confluence):*
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.

Bruce is not really ready for cold testing.&nbsp; But this is hand only cold-testing.

Pending:

battery box

stedim bags for aqualung&nbsp;

Chris P. must work with Brent before spring deployments to solve sampling problem

For Sept deployment need to address high volume issues.

BIOSA integration as a contextual sensor.&nbsp;]]></property>
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<property name="body"><![CDATA[h2. Engineering weekly meeting (Dec 20, 2007)

*Present:* Cheri, Scott, Chris P., Jim, Addie, Chris S.

*Tech Transfer*

&nbsp; &nbsp;Light seals changed?
{color:#3300ff}yes{color}

•&nbsp;&nbsp; &nbsp;Status of slow-running intake
{color:#3300ff}Need to check this out with GG.&nbsp; Science may not be needing it; Chris will Check. Scotts concerned that lower pressure sensor has changed its calibration by 50%.&nbsp; Would like to remove it to look for fouling.&nbsp; Chris mentioned 'blowing-up' a fragile bug because of larger pressure differential; sensor could be culprit.{color}

{color:#ff0000}ACTION:{color} is science finished with GG (Chris S)&nbsp;

{color:#ff0000}ACTION:{color} remove GG lower pressure sensor and examine (Scott)&nbsp;

•&nbsp;&nbsp; &nbsp;Status of manipulator hands.&nbsp; How many needed?&nbsp; How many made?&nbsp; Where are those installed?&nbsp; Waiting on any parts for hand?
{color:#3300ff}Still futzing with first redesigned hand.&nbsp; Very touchy assembly. Have 3 built but have found a problem with cam motor-mount.{color}

{color:#ff0000}ACTION:&nbsp;{color} meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)

•&nbsp;&nbsp; &nbsp;Status of motors and motor-mounts?
{color:#3300ff}Have all motors.&nbsp; Have all mounts.&nbsp; Mike is modifying encoder gears.{color}

•&nbsp;&nbsp; &nbsp;Any questions about published timeline?
{color:#3300ff}Will be using piezo-arrays for all these testings.&nbsp;{color}

{color:#ff0000}ACTION:{color}&nbsp; Need a Gantt chart of instrument usage (Jim)

•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?
{color:#3300ff}they sent a drawing of what they planned on doing (2 weeks ago?).&nbsp; Scott replied; do it.&nbsp; Haven't heard from them yet.{color}

{color:#ff0000}ACTION:{color} call and find out where they are (Scott)

•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?

{color:#ff0000}ACTION:{color} Must check with Jose.&nbsp; He's adding up inventory.&nbsp; Will need enough for 2 cores and 8 MFB and spares (at least 1 full core and enough spares for 8 MFB's\[3 dwarves, 2 R's\]).&nbsp; Tally up, look at production run, and scale up for best economy.&nbsp; Will place order early January. (Scott)

•&nbsp;&nbsp; &nbsp;Discussion of IP tech transfer w/ LLNL?
{color:#3300ff}Update:&nbsp; we have written agreement with LLNL that UH, WHOI, is aproved.&nbsp; Foreign use is unknown and Patrice is looking into it.&nbsp; Valve design TBD{color}

{color:#ff0000}ACTION:{color}&nbsp; Clarify IP on valve design (Chris)&nbsp;

*MFB*
•&nbsp;&nbsp; &nbsp;What will be MFB status as of 12-21-07?
{color:#3300ff}Solid phase extraction working well.&nbsp; Running through lysate coil on AIV.&nbsp; Slug still shows a gradient, first 100ul good, second 100ul (over column) has high concentration.&nbsp; Going to try just pushing 100ul through.&nbsp; Unable to find mixing chambers, so will only take 100, push to and fro a few times and it'll be mixed.&nbsp; Chris P thinks it may be TOO concentrated, bench rocovery is 12-25ug, and extrction is 25ug minimum.&nbsp; Still tweaking this.&nbsp; This will be January focus.&nbsp; Standardize the protocol for this.{color}

•&nbsp;&nbsp; &nbsp;When will all parts be in for 2nd MFB?
{color:#3300ff}All parts are in except MAXON motors.&nbsp;&nbsp; Cheri ordered 33 total, 27 for her and 6 for Addie (who has used 4, 2 are around MBARI) and needs to order 6 more.&nbsp; Cheri will use 24 w/ 1 spare apiece.&nbsp;{color}

{color:#ff0000}ACTION:{color}{color:#000000}&nbsp; place order with MAXON for MFB spares (Addie){color}

•&nbsp;&nbsp; &nbsp;What is left in extraction protocol?&nbsp; {color:#3300ff}Finalization of protocols will be early January.{color}

{color:#3300ff}{*}Chris Scholin hosting CMORE workshop Jan. 14-17 (35 people from OR, HI, WHOI) to define functional requirements for our and other partners CMORE work.*{color}{color:#3300ff}&nbsp; Suggests that we clean up MFB and put on cart, and do a demo run.&nbsp; Get rid of power board and zip tie things and tubing wraps, etc.{color}

{color:#3300ff}Dscussion about LLNL, when they will get a new block to us.&nbsp; If we get the driver block, we should have it out for display.{color}

{color:#3300ff}Discussion about PSV valve.&nbsp; Addie will add the PSV valve.&nbsp; Discussion about connections b/w core and MFB.{color}

{color:#ff0000}ACTION:{color} Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addie will figure out how to connect ports 3, 5, 6 with no bubbles. (Addie)

{color:#ff0000}ACTION:{color}&nbsp; Lubricating syringe.&nbsp; Must be 'upside-down' to prime with no air bubbles.&nbsp; But then could rotate 180 so it retains lubricant. Investigate remounting this right-side up after priming (Addie & Scott)

{color:#ff0000}ACTION:{color}&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (Scott will email)

*Software*
Brent gone until Jan 2nd.

*Sphere and 4K DWSMS*
•&nbsp;&nbsp; &nbsp;Sphere ordered by Jon Erikson on Dec 13, 2007.

*Funny Money Expenditures*
•&nbsp;&nbsp; &nbsp;Currently getting quote on 3 cans/endcaps; do we need for current year?

{color:#3300ff}We have two complete surface moorings (although one can is a 'spare').&nbsp; Will turn off mooring hardware PO from 2006.{color}
•&nbsp;&nbsp; &nbsp;Pucks?

{color:#3300ff}Mike will have a quote tomorrow.{color}
{color:#3300ff}big expenses should go through Chris S for spreading charges among accounts.{color}

*Issues from Doug:*

•&nbsp;&nbsp; &nbsp;Serial numbering of pucks.

{color:#ff0000}ACTION:{color} Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott)

•&nbsp;&nbsp; &nbsp;Image reflections on puck.&nbsp; Still and issue?
{color:#3300ff}no{color}
•&nbsp;&nbsp; &nbsp;Concern on cleanliness of SSfittings off deep chamber
{color:#3300ff}We are only using electrical connctors, not fluid connectors. May have to order fluid fittings for 'box test'.{color}

{color:#ff0000}ACTION:{color} look into need for new fluid fittings and order if necessary (Cheri)

•&nbsp;&nbsp; &nbsp;Pressure pots; rust source?
{color:#3300ff}Will clean and should be okay.{color}

{color:#ff0000}ACTION:{color} Cheri to get pressure pot sizes to figure box structure. (Cheri)

{color:#ff0000}ACTION:&nbsp;{color} Pressure posts. We want this inventory: 2 fives, 2 tens, 2 threes.&nbsp; Must order enough to reach this inventory (Chris P)

•&nbsp;&nbsp; &nbsp;Battery/power issues for spring deployments
{color:#3300ff}stick with alkaline.&nbsp; Do we need more boxes?&nbsp; Need 4 boxes initially.&nbsp; Not working on low power issues.&nbsp; Must order minimum of 1 box of batteries in early 2008.{color}

*4K stuff:*
1. I have lower, more reasonable quotes for the sample chambers, but
they're trepanning solid stock so it's still pricey. It is something
that we could do or have El Camino do instead. I'll need to touch base
with Mike to see if it's worth while. Maybe a competitive quote from El
Cam.
2. We don't have a lot of time (20 weeks lead time on these) but I'm
looking into a steel housing to proof the system before. End caps and
penetrators would still be TI, but $40k would buy a lot.
3. I've made some small (but measureable with an interferometer)
progress on the 1k article.

*Timeline (This schedule is its own page in Confluence):*
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.

{color:#3300ff}Cold testing of Bruce is really just 'hand' cold-testing.&nbsp; Valving and tubing tests commence with Ma{color}ck.

*Items Pending:*

battery box
stedim bags for aqualung&nbsp;
Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp;]]></property>
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<property name="body"><![CDATA[h2. Engineering weekly meeting (Dec 20, 2007)

*Present:* Cheri, Scott, Chris P., Jim, Addie, Chris S.

*Tech Transfer*

&nbsp; &nbsp;Light seals changed?
{color:#3300ff}yes{color}

•&nbsp;&nbsp; &nbsp;Status of slow-running intake
{color:#3300ff}Need to check this out with GG.&nbsp; Science may not be needing it; Chris will Check. Scotts concerned that lower pressure sensor has changed its calibration by 50%.&nbsp; Would like to remove it to look for fouling.&nbsp; Chris mentioned 'blowing-up' a fragile bug because of larger pressure differential; sensor could be culprit.{color}

{color:#ff0000}ACTION:{color} is science finished with GG (Chris S)&nbsp;

{color:#ff0000}ACTION:{color} remove GG lower pressure sensor and examine (Scott)&nbsp;

•&nbsp;&nbsp; &nbsp;Status of manipulator hands.&nbsp; How many needed?&nbsp; How many made?&nbsp; Where are those installed?&nbsp; Waiting on any parts for hand?
{color:#3300ff}Still futzing with first redesigned hand.&nbsp; Very touchy assembly. Have 3 built but have found a problem with cam motor-mount.{color}

{color:#ff0000}ACTION:&nbsp;{color} meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)

•&nbsp;&nbsp; &nbsp;Status of motors and motor-mounts?
{color:#3300ff}Have all motors.&nbsp; Have all mounts.&nbsp; Mike is modifying encoder gears.{color}

•&nbsp;&nbsp; &nbsp;Any questions about published timeline?
{color:#3300ff}Will be using piezo-arrays for all these testings.&nbsp;{color}

{color:#ff0000}ACTION:{color}&nbsp; Need a Gantt chart of instrument usage (Jim)

•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?
{color:#3300ff}they sent a drawing of what they planned on doing (2 weeks ago?).&nbsp; Scott replied; do it.&nbsp; Haven't heard from them yet.{color}

{color:#ff0000}ACTION:{color} call and find out where they are (Scott)

•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?

{color:#ff0000}ACTION:{color} Must check with Jose.&nbsp; He's adding up inventory.&nbsp; Will need enough for 2 cores and 8 MFB and spares (at least 1 full core and enough spares for 8 MFB's\[3 dwarves, 2 R's\]).&nbsp; Tally up, look at production run, and scale up for best economy.&nbsp; Will place order early January. (Scott)

•&nbsp;&nbsp; &nbsp;Discussion of IP tech transfer w/ LLNL?
{color:#3300ff}Update:&nbsp; we have written agreement with LLNL that UH, WHOI, is aproved.&nbsp; Foreign use is unknown and Patrice is looking into it.&nbsp; Valve design TBD{color}

{color:#ff0000}ACTION:{color}&nbsp; Clarify IP on valve design (Chris)&nbsp;

*MFB*
•&nbsp;&nbsp; &nbsp;What will be MFB status as of 12-21-07?
{color:#3300ff}Solid phase extraction working well.&nbsp; Running through lysate coil on AIV.&nbsp; Slug still shows a gradient, first 100ul good, second 100ul (over column) has high concentration.&nbsp; Going to try just pushing 100ul through.&nbsp; Unable to find mixing chambers, so will only take 100, push to and fro a few times and it'll be mixed.&nbsp; Chris P thinks it may be TOO concentrated, bench rocovery is 12-25ug, and extrction is 25ug minimum.&nbsp; Still tweaking this.&nbsp; This will be January focus.&nbsp; Standardize the protocol for this.{color}

•&nbsp;&nbsp; &nbsp;When will all parts be in for 2nd MFB?
{color:#3300ff}All parts are in except MAXON motors.&nbsp;&nbsp; Cheri ordered 33 total, 27 for her and 6 for Addie (who has used 4, 2 are around MBARI) and needs to order 6 more.&nbsp; Cheri will use 24 w/ 1 spare apiece.&nbsp;{color}

{color:#ff0000}ACTION:{color}{color:#000000}&nbsp; place order with MAXON for MFB spares (Addie){color}

•&nbsp;&nbsp; &nbsp;What is left in extraction protocol?&nbsp; {color:#3300ff}Finalization of protocols will be early January.{color}

{color:#3300ff}{*}Chris Scholin hosting CMORE workshop Jan. 14-17 (35 people from OR, HI, WHOI) to define functional requirements for our and other partners CMORE work.*{color}{color:#3300ff}&nbsp; Suggests that we clean up MFB and put on cart, and do a demo run.&nbsp; Get rid of power board and zip tie things and tubing wraps, etc.{color}

{color:#3300ff}Dscussion about LLNL, when they will get a new block to us.&nbsp; If we get the driver block, we should have it out for display.{color}

{color:#3300ff}Discussion about PSV valve.&nbsp; Addie will add the PSV valve.&nbsp; Discussion about connections b/w core and MFB.{color}

{color:#ff0000}ACTION:{color} Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addie will figure out how to connect ports 3, 5, 6 with no bubbles. (Addie)

{color:#ff0000}ACTION:{color}&nbsp; Lubricating syringe.&nbsp; Must be 'upside-down' to prime with no air bubbles.&nbsp; But then could rotate 180 so it retains lubricant. Investigate remounting this right-side up after priming (Addie & Scott)

{color:#ff0000}ACTION:{color}&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (Scott will email)

*Software*
Brent gone until Jan 2nd.

*Sphere and 4K DWSMS*
•&nbsp;&nbsp; &nbsp;Sphere ordered by Jon Erikson on Dec 13, 2007.

*Funny Money Expenditures*
•&nbsp;&nbsp; &nbsp;Currently getting quote on 3 cans/endcaps; do we need for current year?

{color:#3300ff}We have two complete surface moorings (although one can is a 'spare').&nbsp; Will turn off mooring hardware PO from 2006.{color}
•&nbsp;&nbsp; &nbsp;Pucks?
{color:#3300ff}big expenses should go through Chris S for spreading charges among accounts.{color}
{color:#3300ff}Mike will have a quote tomorrow.{color}

*Issues from Doug:*

•&nbsp;&nbsp; &nbsp;Serial numbering of pucks.

{color:#ff0000}ACTION:{color} Collect and inventory all pucks (Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott)

•&nbsp;&nbsp; &nbsp;Image reflections on puck.&nbsp; Still and issue?
{color:#3300ff}no{color}
•&nbsp;&nbsp; &nbsp;Concern on cleanliness of SSfittings off deep chamber
{color:#3300ff}We are only using electrical connctors, not fluid connectors. May have to order fluid fittings for 'box test'.{color}

{color:#ff0000}ACTION:{color} look into need for new fluid fittings and order if necessary (Cheri)

•&nbsp;&nbsp; &nbsp;Pressure pots; rust source?
{color:#3300ff}Will clean and should be okay.{color}

{color:#ff0000}ACTION:{color} Cheri to get pressure pot sizes to figure box structure. (Cheri)

{color:#ff0000}ACTION:&nbsp;{color} Pressure posts. We want this inventory: 2 fives, 2 tens, 2 threes.&nbsp; Must order enough to reach this inventory (Chris P)

•&nbsp;&nbsp; &nbsp;Battery/power issues for spring deployments
{color:#3300ff}stick with alkaline.&nbsp; Do we need more boxes?&nbsp; Need 4 boxes initially.&nbsp; Not working on low power issues.&nbsp; Must order minimum of 1 box of batteries in early 2008.{color}

*4K stuff:*
1. I have lower, more reasonable quotes for the sample chambers, but
they're trepanning solid stock so it's still pricey. It is something
that we could do or have El Camino do instead. I'll need to touch base
with Mike to see if it's worth while. Maybe a competitive quote from El
Cam.
2. We don't have a lot of time (20 weeks lead time on these) but I'm
looking into a steel housing to proof the system before. End caps and
penetrators would still be TI, but $40k would buy a lot.
3. I've made some small (but measureable with an interferometer)
progress on the 1k article.

*Timeline (This schedule is its own page in Confluence):*
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.

{color:#3300ff}Cold testing of Bruce is really just 'hand' cold-testing.&nbsp; Valving and tubing tests commence with Ma{color}ck.

*Items Pending:*

battery box
stedim bags for aqualung&nbsp;
Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp;]]></property>
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<property name="body"><![CDATA[h2. Engineering weekly meeting (Dec 20, 2007)

*Tech Transfer*

•&nbsp;&nbsp; &nbsp;Light seals changed?

yes

•&nbsp;&nbsp; &nbsp;Status of slow-running intake

Need to check this out with GG.&nbsp; Science may not be needing it; Chris will Check. Scotts concerned that lower pressure sensor has changed its calibration by 50%.&nbsp; Would like to remove it to look for fouling.&nbsp; Chris mentioned 'blowing-up' some fragile bug becasue of larger pressure differential

ACTION: is science finished with GG (Chris S)&nbsp;

ACTION: remove GG lower pressure sensor and examine (Scott)&nbsp;

•&nbsp;&nbsp; &nbsp;Status of manipulator hands.&nbsp; How many needed?&nbsp; How many made?&nbsp; Where are those installed?&nbsp; Waiting on any parts for hand?

Still futzing with first redesigned hand.&nbsp; Very touchy assembly.&nbsp;
•&nbsp;&nbsp; &nbsp;Status of motors and motor-mounts?
•&nbsp;&nbsp; &nbsp;Any questions about published timeline?
•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?
•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?
•&nbsp;&nbsp; &nbsp;Discussion of IP tech transfer w/ LLNL?

*MFB*
•&nbsp;&nbsp; &nbsp;What will be MFB status as of 12-21-07?

Solid phase extraction working well.&nbsp; Running through lysate coil on AIV.&nbsp; Slug still shows a gradient, first 100ul good, second 100ul (over column) has high concentration.&nbsp; Going to try just pushing 100ul through.&nbsp; Unable to find mixing chambers, so will only take 100, push to and fro a few times and it'll be mixed.&nbsp; Chris P thinks it may be TOO concentrated, bench rocovery is 12-25ug, and extrction is 25ug minimum.&nbsp; Still tweaking this.&nbsp; This will be January focus.&nbsp; Standardize the protocol for this.
•&nbsp;&nbsp; &nbsp;When will all parts be in for 2nd MFB?

All parts are in except MAXON motors.&nbsp;&nbsp; Cheri ordered 33 total, 27 for her and 6 for Addie (who has used 4, 2 around) and needs to order 6 more(?).&nbsp; Cheri will use 24 w/ 1 spare apiece.&nbsp; ACTION:&nbsp; order from MAXON.



•&nbsp;&nbsp; &nbsp;What is left in extraction protocol?&nbsp; This will all be early January.

Chris Scholin hosting CMORE workshop Jan. 14-17 (35 people from OR, HI, WHOI) to define functional requirements for our and other partners CMORE work.&nbsp; Suggests that we clean up MFB and put on cart, and do a demo run.&nbsp; Get rid of power board and zip tie things and tubing wraps, etc.


Dscussion about LLNL, when they will get a new block to us.&nbsp; If we get the driver block, we should have it out for display.

Discussion about PSV valve.&nbsp; Addie will add the PSV valve.&nbsp; Discussion about connections b/w core and MFB.

ACTION: Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addice will figure out how to connect ports 3, 5, 6 with no bubbles.

ACTION:&nbsp; Lubricating syringe.&nbsp; Must be 'upside-down' to prime with no air bubbles.&nbsp; But then could rotate 180 so it retains lubricant. Investigate remounting this right-side up after priming.


ACTION:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (scot will email)


*Software*
Brent gone until Jan 2nd.

*Sphere and 4K DWSMS*
•&nbsp;&nbsp; &nbsp;Sphere ordered by Jon Erikson on Dec 13, 2007.

Funny Money Expenditures
•&nbsp;&nbsp; &nbsp;Currently getting quote on 3 cans/endcaps; do we need for current year?
•&nbsp;&nbsp; &nbsp;Pucks?
•&nbsp;&nbsp; &nbsp;Other End-of-year expenses?

*Issues from Doug:*

•&nbsp;&nbsp; &nbsp;Serial numbering of pucks.
•&nbsp;&nbsp; &nbsp;Image reflections on puck.&nbsp; Still and issue?
•&nbsp;&nbsp; &nbsp;Concern on cleanliness of SSfittings off deep chamber
•&nbsp;&nbsp; &nbsp;Pressure pots; rust source?
•&nbsp;&nbsp; &nbsp;Battery/power issues for spring deployments
*4K stuff:*
1. I have lower, more reasonable quotes for the sample chambers, but
they're trepanning solid stock so it's still pricey. It is something
that we could do or have El Camino do instead. I'll need to touch base
with Mike to see if it's worth while. Maybe a competitive quote from El
Cam.
2. We don't have a lot of time (20 weeks lead time on these) but I'm
looking into a steel housing to proof the system before. End caps and
penetrators would still be TI, but $40k would buy a lot.
3. I've made some small (but measureable with an interferometer)
progress on the 1k article.

*Timeline (from Confluence):*
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.]]></property>
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<property name="body"><![CDATA[h2. Engineering weekly meeting (Dec 20, 2007)

*Tech Transfer*

•&nbsp;&nbsp; &nbsp;Light seals changed?

yes

•&nbsp;&nbsp; &nbsp;Status of slow-running intake

Need to check this out with GG.&nbsp; Science may not be needing it; Chris will Check. Scotts concerned that lower pressure sensor has changed its calibration by 50%.&nbsp; Would like to remove it to look for fouling.&nbsp; Chris mentioned 'blowing-up' some fragile bug becasue of larger pressure differential

ACTION: is science finished with GG (Chris S)&nbsp;

ACTION: remove GG lower pressure sensor and examine (Scott)&nbsp;

•&nbsp;&nbsp; &nbsp;Status of manipulator hands.&nbsp; How many needed?&nbsp; How many made?&nbsp; Where are those installed?&nbsp; Waiting on any parts for hand?

Still futzing with first redesigned hand.&nbsp; Very touchy assembly. Have 3 built

ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)

•&nbsp;&nbsp; &nbsp;Status of motors and motor-mounts?

Have all motors.&nbsp; Have all mounts.&nbsp; Mike is modifying encoder gears.

•&nbsp;&nbsp; &nbsp;Any questions about published timeline?

Will be using piezo-arrays for all these testing.&nbsp;

ACTION:&nbsp; Need a Gantt chart of instrument usage (Jim)

•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?

they sent a drawing of what they planned on doing (2 weeks ago?).&nbsp; Scott replied; do it.&nbsp; Haven't heard from them yet.

ACTION: call and find out where they are (Scott)

•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?

ACTION: Must check with Jose.&nbsp; He's adding up inventory.&nbsp; Will need enough for 2 cores and 8 MFB and spares (at least 1 full core and enough spares for 8 MFB's\[3 dwarves, 2 R's\]).&nbsp; Tally up, look at production run, and scale up for best economy.&nbsp; Will place order early January.



•&nbsp;&nbsp; &nbsp;Discussion of IP tech transfer w/ LLNL?

Update:&nbsp; we have written agreement with LLNL that UH, WHOI, is aproved.&nbsp; Foreign use is unknown and Patrice is looking into it.&nbsp; Valve design TBD

ACTION:&nbsp; Clarify IP on valve design (Chris)&nbsp;

*MFB*
•&nbsp;&nbsp; &nbsp;What will be MFB status as of 12-21-07?

Solid phase extraction working well.&nbsp; Running through lysate coil on AIV.&nbsp; Slug still shows a gradient, first 100ul good, second 100ul (over column) has high concentration.&nbsp; Going to try just pushing 100ul through.&nbsp; Unable to find mixing chambers, so will only take 100, push to and fro a few times and it'll be mixed.&nbsp; Chris P thinks it may be TOO concentrated, bench rocovery is 12-25ug, and extrction is 25ug minimum.&nbsp; Still tweaking this.&nbsp; This will be January focus.&nbsp; Standardize the protocol for this.
•&nbsp;&nbsp; &nbsp;When will all parts be in for 2nd MFB?

All parts are in except MAXON motors.&nbsp;&nbsp; Cheri ordered 33 total, 27 for her and 6 for Addie (who has used 4, 2 around) and needs to order 6 more(?).&nbsp; Cheri will use 24 w/ 1 spare apiece.&nbsp; ACTION:&nbsp; order from MAXON.

•&nbsp;&nbsp; &nbsp;What is left in extraction protocol?&nbsp; This will all be early January.

Chris Scholin hosting CMORE workshop Jan. 14-17 (35 people from OR, HI, WHOI) to define functional requirements for our and other partners CMORE work.&nbsp; Suggests that we clean up MFB and put on cart, and do a demo run.&nbsp; Get rid of power board and zip tie things and tubing wraps, etc.

Dscussion about LLNL, when they will get a new block to us.&nbsp; If we get the driver block, we should have it out for display.

Discussion about PSV valve.&nbsp; Addie will add the PSV valve.&nbsp; Discussion about connections b/w core and MFB.

ACTION: Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addice will figure out how to connect ports 3, 5, 6 with no bubbles.

ACTION:&nbsp; Lubricating syringe.&nbsp; Must be 'upside-down' to prime with no air bubbles.&nbsp; But then could rotate 180 so it retains lubricant. Investigate remounting this right-side up after priming.

ACTION:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (scot will email)

*Software*
Brent gone until Jan 2nd.

*Sphere and 4K DWSMS*
•&nbsp;&nbsp; &nbsp;Sphere ordered by Jon Erikson on Dec 13, 2007.

Funny Money Expenditures
•&nbsp;&nbsp; &nbsp;Currently getting quote on 3 cans/endcaps; do we need for current year?
•&nbsp;&nbsp; &nbsp;Pucks?
•&nbsp;&nbsp; &nbsp;Other End-of-year expenses?

*Issues from Doug:*

•&nbsp;&nbsp; &nbsp;Serial numbering of pucks.

ACTION: Collect and inventory all pucks (Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott)

•&nbsp;&nbsp; &nbsp;Image reflections on puck.&nbsp; Still and issue?

no
•&nbsp;&nbsp; &nbsp;Concern on cleanliness of SSfittings off deep chamber

We are only using electrical connctors?

ACTION: look into new fluid fittings (Cheri)\\


•&nbsp;&nbsp; &nbsp;Pressure pots; rust source?

Will clean.

ACTION: Cheri to get the sizes to figure box structure. (Cheri)


ACTION:&nbsp; Pressure posts. We want this inventory: 2 fives, 2 tens, 2 threes.&nbsp; Must order enough to reach this inventory (Chris P)


•&nbsp;&nbsp; &nbsp;Battery/power issues for spring deployments


*4K stuff:*
1. I have lower, more reasonable quotes for the sample chambers, but
they're trepanning solid stock so it's still pricey. It is something
that we could do or have El Camino do instead. I'll need to touch base
with Mike to see if it's worth while. Maybe a competitive quote from El
Cam.
2. We don't have a lot of time (20 weeks lead time on these) but I'm
looking into a steel housing to proof the system before. End caps and
penetrators would still be TI, but $40k would buy a lot.
3. I've made some small (but measureable with an interferometer)
progress on the 1k article.

*Timeline (from Confluence):*
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.

Bruce is not really ready for cold testing.&nbsp; But this is hand only cold-testing.]]></property>
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<property name="body"><![CDATA[Distribution list as of 10 May 2010:
\\
\\
|| MFB || PCR Module # || on Core || who gets? || ||
| tombstone | 5 \\ | NEO \\ | MBARI | |
| MFB1 | 1 | Moe | MBARI | |
| MFB2 | \\ | Betty | MBARI | |
| MFB3 | 4 | Gordon | MBARI | |
| MFB4 | 7 \\ | | CMORE | |
| MFB5 | 8 | | U. of Ga \\ | |
| MFB6 | \\ | | Stanford | \\ |
| MFB7 | | | Harvard/Girgius | |
| MFB8 | none | | Harban's | |
| MFB9 | 13 \\ | | Caltech/Orphan | |
| MFB10 | 11 | | SCCWRP | |
| {color:#3366ff}&nbsp;MFB11{color} | 12 | | MBARI | under construction \\ |
| | | | | |
| | Spare: | | | |
| | 14 | | | |
| | Broken?: | | | |
| | 3 | | was originally on Tombstone, but moved #9 there for M0 deployment. Not enough sensitivity.&nbsp; \\ | |
| | 10 | | removed from MFB6.&nbsp; Bleach leak caused flakey connector. \\ | |
| | 9 | | removed from tombstone.&nbsp; Erratic diode readings \\ | |]]></property>
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<property name="body"><![CDATA[h2. Meeting minutes stored in the projectlibrary:&nbsp;

# [Meeting Notes from June 7, 2007|http://oceana.shore.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc]
\\

h2. Meeting minutes stored within Confluence:

# [08nov2007]
# [15Nov2007]
# [29Nov2007]]]></property>
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<property name="body"><![CDATA[[HAB-DA Process Diagram|^G3HABDA-0.1.pptx]Ver 0.1

[HAB-DA Cartridge written protocol|^3G_HABDA_Ver0.1.doc]Ver 0.1

\\  [^G3 Modular Cartridge 05-02-12.pptx] Revised: May 2, 2012]]></property>
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<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.


March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns.
\\

h4.


h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris
\\]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'jar -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application
{panel}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation. Done in three stages
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{jiraissues:https://oceana.mbari.org/jira/sr/jira.issueviews:searchrequest-xml/temp/SearchRequest.xml?&pid=10050&status=1&status=3&status=4&component=10082&sorter/field=issuekey&sorter/order=DESC&sorter/field=priority&sorter/order=DESC&tempMax=1000|anonymous=true}
{panel}


]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| | G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| 1 \\ | Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| 2 | Intake point and Screen \\ | | | | 2 |
| 3 | | | | | |
| 4 | Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| 5 | Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| 6 | Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| 7 | Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| 8 | Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| 9 | Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| 10 | Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| 11 | Cartridge Seals \\ | | | | 2 |
| 12 | \\ | | | | |
| 13 | \\ | \\ | \\ | | |
| 14 | Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| 15 | Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| 16 | Filter Evacuate \\ | * Need to remove seawater <5% of lysis volume.
* In G2, remaining seawater needs to be <100uL
* For 1mL lysis volume, <50uL, or <1 drop.
** Test numbers: Dry filter \+holder, 9.91g
** wet filter (filter holder dry) 9.95g (40 uL)
** no change if vacuumed, no change w/ singe 10ml blow thru
** after 3X 10mL blow thru, 9.92g (10 uL)
** filter appeared to be mostly dry | * Air pressure evac (G2 method)
* Vacuum assist below filter?
* Filter holder is piston assembly, w/ small dead volumes
* Displacement with other fluid? | | 4 |
| 17 | Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| 18 | DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| 19 | Direct Capture \\ | | | | |
| 20 | Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| 21 | Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| 22 | | | | | |
| 23 | Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| 24 | Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| 25 | Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| 26 | Cartridge Actuators \\ | | | | 4 |
| 27 | \\ | \\ | \\ | \\ | |
| 28 | Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| 29 | Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| 30 | | | | | |
| 31 | TRANSFER TO AM | | | | |
| 32 | Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| 33 | AM Selector Injection Loop \\ | | | | 4 \\ |
| 34 | Clean Injection Loop \\ | | | | 4 \\ |
| 35 | Rotor Pass-Thru \\ | | | | 2 |
| 36 | LRAUV Platform Interface \\ | | | | 2 \\ |
| 37 | LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | See model \\
G3LRAUVHousing.sldasm \\ | 2 \\ |
| 38 | | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | * Need to remove seawater <5% of lysis volume.
* In G2, remaining seawater needs to be <100uL
* For 1mL lysis volume, <50uL, or <1 drop.
** Test numbers: Dry filter \+holder, 9.91g
** wet filter (filter holder dry) 9.95g (40 uL)
** no change if vacuumed, no change w/ singe 10ml blow thru
** after 3X 10mL blow thru, 9.92g (10 uL)
** filter appeared to be mostly dry | * Air pressure evac (G2 method)
* Vacuum assist below filter?
* Filter holder is piston assembly, w/ small dead volumes
* Displacement with other fluid? | | 4 |
| Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | See model \\
G3LRAUVHousing.sldasm \\ | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010]]></property>
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</object>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

[ESP Logos]

h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/fluid%20worksheet%20MFB%2014-MAR-07.pdf]
# [Engineering Timeline Q1/Q2 2008]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]

h2. Science]]></property>
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<id name="id">2195835</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]

h2. Engineering 
h4. System Integration
# [Complete system tubing diagram |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/fluid%20worksheet%20MFB%2014-MAR-07.pdf]

h4. Hardware
# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]

h4. Software
# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]

h2. Science]]></property>
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<property name="body"><![CDATA[h3. 2008 Q1/Q2]]></property>
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<property name="body"><![CDATA[#h 2008 Q1/Q2]]></property>
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</property>
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<property name="body"><![CDATA[# 2008 Q1/Q2]]></property>
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<property name="body"><![CDATA[In order to read in data from the ESP, the GUI will use the ESP's log (*real.log*) file as the official 'interface' for data collection.  In order to facilitate this, this page documents what the entries in the log file should look like so that the ESP GUI will not have to make extensive and fragile rules to try and interpret the data.  The esp gui log data should have the following format in the context the [raw log file|ESPAPP:Parsing the Raw ESP Log File Format|Raw Log File Format]:

_EVENT-NAME{_}*,*{_}attribute=value,..._

Notes:
# Time is designated using epoch seconds (number of seconds that have elapsed since January 1, 1970) in _GMT_
# EVENT_NAME is one of the following:
## BEGIN_MISSON
## PHASE_START
## PHASE_END
## PROTOCOL_START
## PROTOCOL_END
## SAMPLE_START
## SAMPLE_END
## CAMERA_SNAP
## END_MISSION
# Attributes are key=value pairs and vary from event to event.  Attributes for the various events are:
## BEGIN_MISSON
### No attributes
### Example: {{BEGIN_MISSION}}
## PHASE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### Example: {{PHASE_START,phase_name=hab}}
## PHASE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS (this is the time that the phase started.  This is necessary due to the fact there are multiple threads the name & start date are the unique key.)
### Example: {{PHASE_END,phase_name=hab,phase_start=1231372399}}
## PROTOCOL_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECDONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### Example: {{PROTOCOL_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1}}
## PROTOCOL_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### Example: {{PROTOCOL_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399}}
## SAMPLE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### target_volume=ZZZZml
### Example: {{SAMPLE_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,target_volume=1000ml}}
## SAMPLE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### sample_volume=ZZZZml
### Example: {{SAMPLE_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,sample_volume=934.1ml}}
## CAMERA_SNAP
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### file_name=ZZZZZZZZZ.tif
### auto_exposure=AAAAAAAs
### Example: {{CAMERA_SNAP,phase_name=hab,phase_start=1231372399,file_name=bac08oct1716h450ml40s.tif,auto_exposure=123.4s}}
{panel:title=Actual log entries}
Rich made the changes to the ruby code to generate the log entries in the following format:
# protocol/BAC.rb
## Thread.log.data "BAC_BACSH1_START"
## Thread.log.data "BAC_BACSH1_START"
## Thread.log.data "BAC_SHORTBACSH2_START"
## Thread.log.data "BAC_SHORTBACSH2_END"
## Thread.log.data "BAC_PHASE_START"
## Thread.log.data "BAC_PHASE_END"
# protocol/samplepass.rb
## Thread.log.data "SAMPLEPASS_LYFIL_START"
## Thread.log.data "SAMPLEPASS_LYFIL_END"
# protocol/PUFM.rb
## Thread.log.data "PUFM_START"
## Thread.log.data "PUFM_END"
## Thread.log.data "PUFM_WITHINITIALPURGE_START"
## Thread.log.data "PUFM_WITHINITIALPURGE_END"
# protocol/HAB.rb
## Thread.log.data "HAB_HABSH1_START"
## Thread.log.data "HAB_HABSH1_END"
## Thread.log.data "HAB_SHORTHABSH2_START"
## Thread.log.data "HAB_SHORTHABSH2_END"
## Thread.log.data "HAB_PHASE_START"
## Thread.log.data "HAB_PHASE_END"
# protocol/wcr.rb
## Thread.log.data "WCR_PROTOCOL_START," + " volume=#\{sampleVolume\}"
## Thread.log.data "WCR_PROTOCOL_END"
# protocol/DA.rb
## Thread.log.data "DA_DAEXTRACT_START"
## Thread.log.data "DA_DAEXTRACT_END"
## Thread.log.data "DA_START"
## Thread.log.data "DA_END"
## Thread.log.data "DA_SHORTDA_START"
## Thread.log.data "DA_SHORTDA_END"
## Thread.log.data "DA_HAB4DA_START"
## Thread.log.data "DA_HAB4DA_END"
## Thread.log.data "DA_HABDA_START"
## Thread.log.data "DA_HABDA_END"
# protocol/utilities.rb
## Thread.log.data "PROTOCOLARGS, assay=#\{opts\[:assay\]\}, maxvolume=#\{sampleVolume.first\}, wcrmaxvolume=#\{sampleVolume.last\}"
## Thread.log.data "INITIALPURGE_START"
## Thread.log.data "INITIALPURGE_END"
## Thread.log.data "FINALPURGE_START"
## Thread.log.data "FINALPURGE_END"
# protocol/LARV.rb
## Thread.log.data "LARV_LARVSH1_START"
## Thread.log.data "LARV_LARVSH1_END"
## Thread.log.data "LARV_SHORTLARVSH2_START"
## Thread.log.data "LARV_SHORTLARVSH2_END"
## Thread.log.data "LARV_PHASE_START"
## Thread.log.data "LARV_PHASE_END"
## Thread.log.data "LARV_PHASE_WITHPURGE_START"
## Thread.log.data "LARV_PHASE_WITHPURGE_END"
# protocol/sh2.rb
## Thread.log.data "SH2_PROTOCOL_START"
## Thread.log.data "SH2_PROTOCOL_END"
## Thread.log.data "SH2_SHORTSH2_START"
## Thread.log.data "SH2_SHORTSH2_END"
## Thread.log.data "SH2_SH2CORE_START, phase=#\{phase\},label=#\{label\}"
## Thread.log.data "SH2_SH2CORE_END"
# protocol/sh1.rb
## Thread.log.data "SH1_PROTOCOL_START"
## Thread.log.data "SH1_PROTOCOL_END"
## Thread.log.data "SH1_COLLECTSAMPLE, " + "volume=#\{sampleVolume\}, bubblepoint=#\{collectionSampler.bubblePt\}"
## Thread.log.data "SH1_COLLECTSAMPLE_COMPLETE"
## Thread.log.data "SH1_LYSING, volume=#\{lysisVolume\},solution=#\{lysisSolution\}"
# protocol/MFB.rb
## Thread.log.data "MFB_MFBSH1_START"
## Thread.log.data "MFB_MFBSH1_END"
## Thread.log.data "MFB_START"
## Thread.log.data "MFB_END"
# protocol/KAR.rb
## Thread.log.data "KAR_KARSH1_START"
## Thread.log.data "KAR_KARSH1_START"
## Thread.log.data "KAR_SHORTKARSH2_START"
## Thread.log.data "KAR_SHORTKARSH2_END"
## Thread.log.data "KAR_PHASE_START"
## Thread.log.data "KAR_PHASE_END"
# lib/esp.rb
## Thread.log.data "LIB_ESP_IRB_START, string=" + $0
## Thread.log.data "LIB_ESP_CONFIG,instrumentname=#\{Name\}, cfgpath=#\{ConfigPath\}"
## Thread.log.data "LIB_ESP_IRB_END" 
## Thread.log.data "LIB_ESP_APPLICATION_START, string=" + $0
## Thread.log.data "LIB_ESP_CONFIG, instrumentname=#\{Name\}, cfgpath=#\{ConfigPath\}"
## Thread.log.data "LIB_ESP_APPLICATION_END" 
# lib/cmdserver.rb
## Thread.log.data "LIB_CMDSERVER_ABORTMISSION" + reason
## Thread.log.data "CAMERA_SNAP, " + "string=#\{instance\}: #\{SNAP\} #\{args\}"
## Thread.log.data "CAMERA_OUTPUT_" + myn.to_s + ", string= " + line 
{note}
above should expand to:
{noformat}
      CAMERA_OUTPUT_1, string=Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
      CAMERA_OUTPUTA_2, string=Exposing 348x260 pixel 16-bit image for 25.668 seconds
      CAMERA_OUTPUT_3, string=/var/log/rich/larv07oct3015h50ml2.5s.tif: TIFF Upload Complete
{noformat}
{note}
# utils/puckmoves.rb
## Thread.log.data "PUCKMOVES_LOADCLAMP, " + 
{note}
above expand to: 
{noformat}
PUCKMOVES_UNLOADCLAMP, source= , pucknumber= ,tube= , clamp=
{noformat}
{note}
## Thread.log.data "PUCKMOVES_LOADCLAMP_EMPTYTUBE, tube=#\{tube\}"
## Thread.log.data "PUCKMOVES_UNLOADCLAMP, " + guiMsg % \[source.label, clamp.name, toTube\]
{note}
above expand to: 
{noformat}
PUCKMOVES_UNLOADCLAMP, source= , clamp= , tube=
{noformat}
{note}
# utils/misc.rb
## Thread.log.data "MISC_STORAGE_SELECTTUBE_TO"
## Thread.log.data "MISC_STORAGE_SELECTTUBE"
## Thread.log.data "MISC_STORAGE_SRCTUBE, tube=" + startingTube.to_s
## Thread.log.data "MISC_SRCTUBE"
## Thread.log.data "MISC_DSTTUBE" 
# utils/sampler.rb
## Thread.log.data "SAMPLER_SAMPLED, " + "volume=%.1f" % sampledVol
# mission/08sep.rb
## Thread.log.data "MISSION_START, esp=#\{ESP::Name\}, mission=#\{ESP::Mission\}, starttube=#\{startTube\}, fromtube=#\{fromTube\}"
## Thread.log.data "MISSION_END, esp=#\{ESP::Name\}, mission=#\{ESP::Mission\}"
{panel}]]></property>
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<property name="body"><![CDATA[In order to read in data from the ESP, the GUI will use the ESP's log (*real.log*) file as the official 'interface' for data collection.  In order to facilitate this, this page documents what the entries in the log file should look like so that the ESP GUI will not have to make extensive and fragile rules to try and interpret the data.  The esp gui log data should have the following format in the context the [raw log file|ESPAPP:Parsing the Raw ESP Log File Format|Raw Log File Format]:

{section}
{column:width=50%}
_EVENT-NAME{_}*,*{_}attribute=value,..._

Notes:
# Time is designated using epoch seconds (number of seconds that have elapsed since January 1, 1970) in _GMT_
# EVENT_NAME is one of the following:
## BEGIN_MISSON
## PHASE_START
## PHASE_END
## PROTOCOL_START
## PROTOCOL_END
## SAMPLE_START
## SAMPLE_END
## CAMERA_SNAP
## END_MISSION
# Attributes are key=value pairs and vary from event to event.  Attributes for the various events are:
## BEGIN_MISSON
### No attributes
### Example: {{BEGIN_MISSION}}
## PHASE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### Example: {{PHASE_START,phase_name=hab}}
## PHASE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS (this is the time that the phase started.  This is necessary due to the fact there are multiple threads the name & start date are the unique key.)
### Example: {{PHASE_END,phase_name=hab,phase_start=1231372399}}
## PROTOCOL_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECDONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### Example: {{PROTOCOL_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1}}
## PROTOCOL_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### Example: {{PROTOCOL_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399}}
## SAMPLE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### target_volume=ZZZZml
### Example: {{SAMPLE_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,target_volume=1000ml}}
## SAMPLE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### sample_volume=ZZZZml
### Example: {{SAMPLE_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,sample_volume=934.1ml}}
## CAMERA_SNAP
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### file_name=ZZZZZZZZZ.tif
### auto_exposure=AAAAAAAs
### Example: {{CAMERA_SNAP,phase_name=hab,phase_start=1231372399,file_name=bac08oct1716h450ml40s.tif,auto_exposure=123.4s}}
{column}
{column}
{panel:title=Actual log entries}
Rich made the changes to the ruby code to generate the log entries in the following format:
# ./protocol/BAC.rb:  Thread.log.data "BAC_BACSH1_START"
# ./protocol/BAC.rb:  Thread.log.data "BAC_BACSH1_START"
# ./protocol/BAC.rb:  Thread.log.data "BAC_SHORTBACSH2_START"
# ./protocol/BAC.rb:  Thread.log.data "BAC_SHORTBACSH2_END"
# ./protocol/BAC.rb:  Thread.log.data "BAC_PHASE_START"
# ./protocol/BAC.rb:  Thread.log.data "BAC_PHASE_END"
# ./protocol/samplepass.rb:  Thread.log.data "SAMPLEPASS_LYFIL_START"
# ./protocol/samplepass.rb:  Thread.log.data "SAMPLEPASS_LYFIL_END"
# ./protocol/PUFM.rb:  Thread.log.data "PUFM_START"
# ./protocol/PUFM.rb:  Thread.log.data "PUFM_END"
# ./protocol/PUFM.rb:  Thread.log.data "PUFM_WITHINITIALPURGE_START"
# ./protocol/PUFM.rb:  Thread.log.data "PUFM_WITHINITIALPURGE_END"
# ./protocol/HAB.rb:  Thread.log.data "HAB_HABSH1_START"
# ./protocol/HAB.rb:  Thread.log.data "HAB_HABSH1_END"
# ./protocol/HAB.rb:  Thread.log.data "HAB_SHORTHABSH2_START"
# ./protocol/HAB.rb:  Thread.log.data "HAB_SHORTHABSH2_END"
# ./protocol/HAB.rb:  Thread.log.data "HAB_PHASE_START"
# ./protocol/HAB.rb:  Thread.log.data "HAB_PHASE_END"
# ./protocol/wcr.rb:  Thread.log.data "WCR_PROTOCOL_START," + " volume=#\{sampleVolume\}"
# ./protocol/wcr.rb:  Thread.log.data "WCR_PROTOCOL_END"
# ./protocol/DA.rb:  Thread.log.data "DA_DAEXTRACT_START"
# ./protocol/DA.rb:  Thread.log.data "DA_DAEXTRACT_END"
# ./protocol/DA.rb:  Thread.log.data "DA_START"
# ./protocol/DA.rb:  Thread.log.data "DA_END"
# ./protocol/DA.rb:  Thread.log.data "DA_SHORTDA_START"
# ./protocol/DA.rb:  Thread.log.data "DA_SHORTDA_END"
# ./protocol/DA.rb:  Thread.log.data "DA_HAB4DA_START"
# ./protocol/DA.rb:  Thread.log.data "DA_HAB4DA_END"
# ./protocol/DA.rb:  Thread.log.data "DA_HABDA_START"
# ./protocol/DA.rb:  Thread.log.data "DA_HABDA_END"
# ./protocol/utilities.rb:  Thread.log.data "PROTOCOLARGS, assay=#\{opts\[:assay\]\}, maxvolume=#\{sampleVolume.first\}, wcrmaxvolume=#\{sampleVolume.last\}"
# ./protocol/utilities.rb:  Thread.log.data "INITIALPURGE_START"
# ./protocol/utilities.rb:  Thread.log.data "INITIALPURGE_END"
# ./protocol/utilities.rb:  Thread.log.data "FINALPURGE_START"
# ./protocol/utilities.rb:  Thread.log.data "FINALPURGE_END"
# ./protocol/LARV.rb:  Thread.log.data "LARV_LARVSH1_START"
# ./protocol/LARV.rb:  Thread.log.data "LARV_LARVSH1_END"
# ./protocol/LARV.rb:  Thread.log.data "LARV_SHORTLARVSH2_START"
# ./protocol/LARV.rb:  Thread.log.data "LARV_SHORTLARVSH2_END"
# ./protocol/LARV.rb:  Thread.log.data "LARV_PHASE_START"
# ./protocol/LARV.rb:  Thread.log.data "LARV_PHASE_END"
# ./protocol/LARV.rb:  Thread.log.data "LARV_PHASE_WITHPURGE_START"
# ./protocol/LARV.rb:  Thread.log.data "LARV_PHASE_WITHPURGE_END"
# ./protocol/sh2.rb:  Thread.log.data "SH2_PROTOCOL_START"
# ./protocol/sh2.rb:  Thread.log.data "SH2_PROTOCOL_END"
# ./protocol/sh2.rb:  Thread.log.data "SH2_SHORTSH2_START"
# ./protocol/sh2.rb:  Thread.log.data "SH2_SHORTSH2_END"
# ./protocol/sh2.rb:  Thread.log.data "SH2_SH2CORE_START, phase=#\{phase\},label=#\{label\}"
# ./protocol/sh2.rb:  Thread.log.data "SH2_SH2CORE_END"
# ./protocol/sh1.rb:  Thread.log.data "SH1_PROTOCOL_START"
# ./protocol/sh1.rb:  Thread.log.data "SH1_PROTOCOL_END"
# ./protocol/sh1.rb:  Thread.log.data "SH1_COLLECTSAMPLE, " + "volume=#\{sampleVolume\}, bubblepoint=#\{collectionSampler.bubblePt\}"
# ./protocol/sh1.rb:  Thread.log.data "SH1_COLLECTSAMPLE_COMPLETE"
# ./protocol/sh1.rb:  Thread.log.data "SH1_LYSING, volume=#\{lysisVolume\},solution=#\{lysisSolution\}"
# ./protocol/MFB.rb:  Thread.log.data "MFB_MFBSH1_START"
# ./protocol/MFB.rb:  Thread.log.data "MFB_MFBSH1_END"
# ./protocol/MFB.rb:  Thread.log.data "MFB_START"
# ./protocol/MFB.rb:  Thread.log.data "MFB_END"
# ./protocol/KAR.rb:  Thread.log.data "KAR_KARSH1_START"
# ./protocol/KAR.rb:  Thread.log.data "KAR_KARSH1_START"
# ./protocol/KAR.rb:  Thread.log.data "KAR_SHORTKARSH2_START"
# ./protocol/KAR.rb:  Thread.log.data "KAR_SHORTKARSH2_END"
# ./protocol/KAR.rb:  Thread.log.data "KAR_PHASE_START"
# ./protocol/KAR.rb:  Thread.log.data "KAR_PHASE_END"
# ./lib/esp.rb:      Thread.log.data "LIB_ESP_IRB_START, string=" + $0
# ./lib/esp.rb:      Thread.log.data "LIB_ESP_CONFIG,instrumentname=#\{Name\}, cfgpath=#\{ConfigPath\}"
# ./lib/esp.rb:      Thread.log.data "LIB_ESP_IRB_END" 
# ./lib/esp.rb:      Thread.log.data "LIB_ESP_APPLICATION_START, string=" + $0
# ./lib/esp.rb:      Thread.log.data "LIB_ESP_CONFIG, instrumentname=#\{Name\}, cfgpath=#\{ConfigPath\}"
# ./lib/esp.rb:      Thread.log.data "LIB_ESP_APPLICATION_END" 
# ./lib/cmdserver.rb:  Thread.log.data "LIB_CMDSERVER_ABORTMISSION" + reason
# ./lib/camera.rb:      Thread.log.data "CAMERA_SNAP, " + "string=#\{instance\}: #\{SNAP\} #\{args\}"
# ./lib/camera.rb:      Thread.log.data "CAMERA_OUTPUT_" + myn.to_s + ", string= " + line 
{note}
above should expand to:
{noformat}
      CAMERA_OUTPUT_1, string=Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
      CAMERA_OUTPUTA_2, string=Exposing 348x260 pixel 16-bit image for 25.668 seconds
      CAMERA_OUTPUT_3, string=/var/log/rich/larv07oct3015h50ml2.5s.tif: TIFF Upload Complete
{noformat}
{note}
# ./utils/puckmoves.rb:      Thread.log.data "PUCKMOVES_LOADCLAMP, " + 
{note}
above expand to: 
{noformat}
PUCKMOVES_UNLOADCLAMP, source= , pucknumber= ,tube= , clamp=
{noformat}
{note}
# ./utils/puckmoves.rb:      Thread.log.data "PUCKMOVES_LOADCLAMP_EMPTYTUBE, tube=#\{tube\}"
# ./utils/puckmoves.rb:    Thread.log.data "PUCKMOVES_UNLOADCLAMP, " + guiMsg % \[source.label, clamp.name, toTube\]
{note}
above expand to: 
{noformat}
PUCKMOVES_UNLOADCLAMP, source= , clamp= , tube=
{noformat}
{note}
# ./utils/misc.rb:   Thread.log.data "MISC_STORAGE_SELECTTUBE_TO"
# ./utils/misc.rb:    Thread.log.data "MISC_STORAGE_SELECTTUBE"
# ./utils/misc.rb:    Thread.log.data "MISC_STORAGE_SRCTUBE, tube=" + startingTube.to_s
# ./utils/misc.rb:  Thread.log.data "MISC_SRCTUBE"
# ./utils/misc.rb:  Thread.log.data "MISC_DSTTUBE" 
# ./utils/sampler.rb:    Thread.log.data "SAMPLER_SAMPLED, " + "volume=%.1f" % sampledVol
# ./mission/08sep.rb:  Thread.log.data "MISSION_START, esp=#\{ESP::Name\}, mission=#\{ESP::Mission\}, starttube=#\{startTube\}, fromtube=#\{fromTube\}"
# ./mission/08sep.rb:  Thread.log.data "MISSION_END, esp=#\{ESP::Name\}, mission=#\{ESP::Mission\}"
{panel}
{column}
{section}
]]></property>
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<property name="body"><![CDATA[In order to read in data from the ESP, the GUI will use the ESP's log (*real.log*) file as the official 'interface' for data collection.  In order to facilitate this, this page documents what the entries in the log file should look like so that the ESP GUI will not have to make extensive and fragile rules to try and interpret the data.  The esp gui log data should have the following format in the context the [raw log file|ESPAPP:Parsing the Raw ESP Log File Format|Raw Log File Format]:

{section}
{column:width=50%}
_EVENT-NAME{_}*,*{_}attribute=value,..._

Notes:
# Time is designated using epoch seconds (number of seconds that have elapsed since January 1, 1970) in _GMT_
# EVENT_NAME is one of the following:
## BEGIN_MISSON
## PHASE_START
## PHASE_END
## PROTOCOL_START
## PROTOCOL_END
## SAMPLE_START
## SAMPLE_END
## CAMERA_SNAP
## END_MISSION
# Attributes are key=value pairs and vary from event to event.  Attributes for the various events are:
## BEGIN_MISSON
### No attributes
### Example: {{BEGIN_MISSION}}
## PHASE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### Example: {{PHASE_START,phase_name=hab}}
## PHASE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS (this is the time that the phase started.  This is necessary due to the fact there are multiple threads the name & start date are the unique key.)
### Example: {{PHASE_END,phase_name=hab,phase_start=1231372399}}
## PROTOCOL_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECDONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### Example: {{PROTOCOL_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1}}
## PROTOCOL_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### Example: {{PROTOCOL_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399}}
## SAMPLE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### target_volume=ZZZZml
### Example: {{SAMPLE_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,target_volume=1000ml}}
## SAMPLE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### sample_volume=ZZZZml
### Example: {{SAMPLE_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,sample_volume=934.1ml}}
## CAMERA_SNAP
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### file_name=ZZZZZZZZZ.tif
### auto_exposure=AAAAAAAs
### Example: {{CAMERA_SNAP,phase_name=hab,phase_start=1231372399,file_name=bac08oct1716h450ml40s.tif,auto_exposure=123.4s}}
{column}
{column}
{panel:title=Actual log entries}
Rich made the changes to the ruby code to generate the log entries in the following format:
# protocol/BAC.rb
## Thread.log.data "BAC_BACSH1_START"
## Thread.log.data "BAC_BACSH1_START"
## Thread.log.data "BAC_SHORTBACSH2_START"
## Thread.log.data "BAC_SHORTBACSH2_END"
## Thread.log.data "BAC_PHASE_START"
## Thread.log.data "BAC_PHASE_END"
# protocol/samplepass.rb
## Thread.log.data "SAMPLEPASS_LYFIL_START"
## Thread.log.data "SAMPLEPASS_LYFIL_END"
# protocol/PUFM.rb
## Thread.log.data "PUFM_START"
## Thread.log.data "PUFM_END"
## Thread.log.data "PUFM_WITHINITIALPURGE_START"
## Thread.log.data "PUFM_WITHINITIALPURGE_END"
# protocol/HAB.rb
## Thread.log.data "HAB_HABSH1_START"
## Thread.log.data "HAB_HABSH1_END"
## Thread.log.data "HAB_SHORTHABSH2_START"
## Thread.log.data "HAB_SHORTHABSH2_END"
## Thread.log.data "HAB_PHASE_START"
## Thread.log.data "HAB_PHASE_END"
# protocol/wcr.rb
## Thread.log.data "WCR_PROTOCOL_START," + " volume=#\{sampleVolume\}"
## Thread.log.data "WCR_PROTOCOL_END"
# protocol/DA.rb
## Thread.log.data "DA_DAEXTRACT_START"
## Thread.log.data "DA_DAEXTRACT_END"
## Thread.log.data "DA_START"
## Thread.log.data "DA_END"
## Thread.log.data "DA_SHORTDA_START"
## Thread.log.data "DA_SHORTDA_END"
## Thread.log.data "DA_HAB4DA_START"
## Thread.log.data "DA_HAB4DA_END"
## Thread.log.data "DA_HABDA_START"
## Thread.log.data "DA_HABDA_END"
# protocol/utilities.rb
## Thread.log.data "PROTOCOLARGS, assay=#\{opts\[:assay\]\}, maxvolume=#\{sampleVolume.first\}, wcrmaxvolume=#\{sampleVolume.last\}"
## Thread.log.data "INITIALPURGE_START"
## Thread.log.data "INITIALPURGE_END"
## Thread.log.data "FINALPURGE_START"
## Thread.log.data "FINALPURGE_END"
# protocol/LARV.rb
## Thread.log.data "LARV_LARVSH1_START"
## Thread.log.data "LARV_LARVSH1_END"
## Thread.log.data "LARV_SHORTLARVSH2_START"
## Thread.log.data "LARV_SHORTLARVSH2_END"
## Thread.log.data "LARV_PHASE_START"
## Thread.log.data "LARV_PHASE_END"
## Thread.log.data "LARV_PHASE_WITHPURGE_START"
## Thread.log.data "LARV_PHASE_WITHPURGE_END"
# protocol/sh2.rb
## Thread.log.data "SH2_PROTOCOL_START"
## Thread.log.data "SH2_PROTOCOL_END"
## Thread.log.data "SH2_SHORTSH2_START"
## Thread.log.data "SH2_SHORTSH2_END"
## Thread.log.data "SH2_SH2CORE_START, phase=#\{phase\},label=#\{label\}"
## Thread.log.data "SH2_SH2CORE_END"
# protocol/sh1.rb
## Thread.log.data "SH1_PROTOCOL_START"
## Thread.log.data "SH1_PROTOCOL_END"
## Thread.log.data "SH1_COLLECTSAMPLE, " + "volume=#\{sampleVolume\}, bubblepoint=#\{collectionSampler.bubblePt\}"
## Thread.log.data "SH1_COLLECTSAMPLE_COMPLETE"
## Thread.log.data "SH1_LYSING, volume=#\{lysisVolume\},solution=#\{lysisSolution\}"
# protocol/MFB.rb
## Thread.log.data "MFB_MFBSH1_START"
## Thread.log.data "MFB_MFBSH1_END"
## Thread.log.data "MFB_START"
## Thread.log.data "MFB_END"
# protocol/KAR.rb
## Thread.log.data "KAR_KARSH1_START"
## Thread.log.data "KAR_KARSH1_START"
## Thread.log.data "KAR_SHORTKARSH2_START"
## Thread.log.data "KAR_SHORTKARSH2_END"
## Thread.log.data "KAR_PHASE_START"
## Thread.log.data "KAR_PHASE_END"
# lib/esp.rb
## Thread.log.data "LIB_ESP_IRB_START, string=" + $0
## Thread.log.data "LIB_ESP_CONFIG,instrumentname=#\{Name\}, cfgpath=#\{ConfigPath\}"
## Thread.log.data "LIB_ESP_IRB_END" 
## Thread.log.data "LIB_ESP_APPLICATION_START, string=" + $0
## Thread.log.data "LIB_ESP_CONFIG, instrumentname=#\{Name\}, cfgpath=#\{ConfigPath\}"
## Thread.log.data "LIB_ESP_APPLICATION_END" 
# lib/cmdserver.rb
## Thread.log.data "LIB_CMDSERVER_ABORTMISSION" + reason
## Thread.log.data "CAMERA_SNAP, " + "string=#\{instance\}: #\{SNAP\} #\{args\}"
## Thread.log.data "CAMERA_OUTPUT_" + myn.to_s + ", string= " + line 
{note}
above should expand to:
{noformat}
      CAMERA_OUTPUT_1, string=Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
      CAMERA_OUTPUTA_2, string=Exposing 348x260 pixel 16-bit image for 25.668 seconds
      CAMERA_OUTPUT_3, string=/var/log/rich/larv07oct3015h50ml2.5s.tif: TIFF Upload Complete
{noformat}
{note}
# utils/puckmoves.rb
## Thread.log.data "PUCKMOVES_LOADCLAMP, " + 
{note}
above expand to: 
{noformat}
PUCKMOVES_UNLOADCLAMP, source= , pucknumber= ,tube= , clamp=
{noformat}
{note}
## Thread.log.data "PUCKMOVES_LOADCLAMP_EMPTYTUBE, tube=#\{tube\}"
## Thread.log.data "PUCKMOVES_UNLOADCLAMP, " + guiMsg % \[source.label, clamp.name, toTube\]
{note}
above expand to: 
{noformat}
PUCKMOVES_UNLOADCLAMP, source= , clamp= , tube=
{noformat}
{note}
# utils/misc.rb
## Thread.log.data "MISC_STORAGE_SELECTTUBE_TO"
## Thread.log.data "MISC_STORAGE_SELECTTUBE"
## Thread.log.data "MISC_STORAGE_SRCTUBE, tube=" + startingTube.to_s
## Thread.log.data "MISC_SRCTUBE"
## Thread.log.data "MISC_DSTTUBE" 
# utils/sampler.rb
## Thread.log.data "SAMPLER_SAMPLED, " + "volume=%.1f" % sampledVol
# mission/08sep.rb
## Thread.log.data "MISSION_START, esp=#\{ESP::Name\}, mission=#\{ESP::Mission\}, starttube=#\{startTube\}, fromtube=#\{fromTube\}"
## Thread.log.data "MISSION_END, esp=#\{ESP::Name\}, mission=#\{ESP::Mission\}"
{panel}
{column}
{section}
]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.12|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.1%202%2011_19_2007.doc]

h3. &nbsp;Fluidics Construction
# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram11-19-07.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]

h3. Engineering

# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
h4. Software Issues
# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]

h3. Science]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]

h3. Engineering

# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Complete system tubing diagram |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/fluid%20worksheet%20MFB%2014-MAR-07.pdf]
# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
h4. Software Issues
# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]

h3. Science]]></property>
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<property name="body"><![CDATA[In order to read in data from the ESP, the GUI will use the ESP's log (*real.log*) file as the official 'interface' for data collection.  In order to facilitate this, this page documents what the entries in the log file should look like so that the ESP GUI will not have to make extensive and fragile rules to try and interpret the data.  The esp gui log data should have the following format in the context the [raw log file|ESPAPP:Parsing the Raw ESP Log File Format|Raw Log File Format]:

_EVENT-NAME{_}*,*{_}attribute=value,..._

Notes:
# Time is designated using epoch seconds (number of seconds that have elapsed since January 1, 1970) in _GMT_
# EVENT_NAME is one of the following:
## BEGIN_MISSON
## PHASE_START
## PHASE_END
## PROTOCOL_START
## PROTOCOL_END
## SAMPLE_START
## SAMPLE_END
## CAMERA_SNAP
## END_MISSION
# Attributes are key=value pairs and vary from event to event.  Attributes for the various events are:
## BEGIN_MISSON
### No attributes
### Example: {{BEGIN_MISSION}}
## PHASE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### Example: {{PHASE_START,phase_name=hab}}
## PHASE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS (this is the time that the phase started.  This is necessary due to the fact there are multiple threads the name & start date are the unique key.)
### Example: {{PHASE_END,phase_name=hab,phase_start=1231372399}}
## PROTOCOL_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECDONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### Example: {{PROTOCOL_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1}}
## PROTOCOL_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### Example: {{PROTOCOL_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399}}
## SAMPLE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### target_volume=ZZZZml
### Example: {{SAMPLE_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,target_volume=1000ml}}
## SAMPLE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### sample_volume=ZZZZml
### Example: {{SAMPLE_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,sample_volume=934.1ml}}
## CAMERA_SNAP
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### file_name=ZZZZZZZZZ.tif
### auto_exposure=AAAAAAAs
### Example: {{CAMERA_SNAP,phase_name=hab,phase_start=1231372399,file_name=bac08oct1716h450ml40s.tif,auto_exposure=123.4s}}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]

h3. Engineering
h4. System Integration
# [Complete system tubing diagram |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/fluid%20worksheet%20MFB%2014-MAR-07.pdf]

h4. Hardware
# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
h4. Software 
# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]

h3. Science]]></property>
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<property name="body"><![CDATA[h2. Engineering weekly meeting (Nov 29, 2007)

Present: Birch, Harris, Scholin, Everlove, Pargett, Roman&nbsp;

*Tech Transfer*
•&nbsp;&nbsp; &nbsp;Status of Bruce and Mack (and Moe)
•&nbsp;&nbsp; &nbsp;New hand construction update
•&nbsp;&nbsp; &nbsp;Status of new motors/ new motor brackets
•&nbsp;&nbsp; &nbsp;Cepheid coming Friday?

{color:#0033ff}Bruce and Mack are 97% assembled.&nbsp; Both lack hand, which only has slider issue to resolve, and all can be modified.&nbsp; Have ordered more blue nipples and tubing; should arrive end of this week (tomorrow?).&nbsp; 27 Maxon motors shipped yesterday.&nbsp; El Camino has not started machining new motor brackets because they lost our PO and the job fell out of que.&nbsp; Mike Parker will push to make them meet their original Dec. delivery date.{color}

{color:#0033ff}Cheri to order enough syringes to completely outfit Bruce, Mack, Moe, plus have a spare set.&nbsp; These are COTS.&nbsp; Scott still working to get custom, cold-rated syringes built.&nbsp; Break charge in thirds among 800560, 703506, 900612.{color}

{color:#0033ff}New motors to be placed on Bruce, Mack, and Moe; no changes to NEO and GG.&nbsp; Dwarf boards--we have enough for Moe, but then no extras.&nbsp; Must meet with Scott about new order.{color}

{color:#0033ff}Cepheid IS arriving for visit tomorrow.&nbsp;{color}

Chris&nbsp;

*MFB*

•&nbsp;&nbsp; &nbsp;Status of adding AIV and new ASV
•&nbsp;&nbsp; &nbsp;Mounting of solid-phase extraction hardware
•&nbsp;&nbsp; &nbsp;Status of new script development
•&nbsp;&nbsp; &nbsp;Heater block sent to LLNL
•&nbsp;&nbsp; &nbsp;Prediction for 12-21-07?

Software
•&nbsp;&nbsp; &nbsp;Tracing the Ruby garbage error...
•&nbsp;&nbsp; &nbsp;Plan for low power processor visit
•&nbsp;&nbsp; &nbsp;Progress of Bob Herlien on MFB drivers?
•&nbsp;&nbsp; &nbsp;Progress of Rich Schramm on GUI?
•&nbsp;&nbsp; &nbsp;JIRA?

Sphere and 4K DWSM
•&nbsp;&nbsp; &nbsp;Ordering sphere
•&nbsp;&nbsp; &nbsp;Still awaiting machining quote from Hanard Machining, Oregon.
•&nbsp;&nbsp; &nbsp;DWSM---need for mechanical design (Doug's return?)]]></property>
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<property name="body"><![CDATA[h2.  Engineering weekly meeting (Nov 29, 2007)]]></property>
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<property name="body"><![CDATA[h2. Meeting minutes stored in the projectlibrary:&nbsp;
# [Meeting Notes from June 7, 2007|http://oceana.shore.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc]
\\

h2. Meeting minutes stored within Confluence:
# [08nov2007]
# [15Nov2007]]]></property>
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<property name="body"><![CDATA[You have four choices:

[B&W .PDF|B&W .PDF|black & white PDF]

B&W .Tiff

Color .PDF

Color .Tiff ]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">16220270</id>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://predator.shore.mbari.org/esp_gui/launch.jnlp]Project Documentation:

h3. Other Documents
# [Documents|ProjectDocuments]
# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
## [ESP GUI Demo and Questions|2007_09_05]
# [Presentations|ProjectPresentations]
# [Tasks]
# [Data Model]
# [Developer Documentation]

h3. Bug Tracking
# [JIRA Issue Tracker|http://oceana.shore.mbari.org:8082/browse/ESPAPP]

]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.\\]]></property>
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<property name="body"><![CDATA[Here is the Logo:
\\
!ESP logo color.jpg|thumbnail!
You have four choices:

[B&W .PDF|B&W .PDF|black & white PDF]

B&W .Tiff

Color .PDF

Color .Tiff
[Tiff image|^ESP logo color.tif]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">16220275</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">16253040</id>
<property name="body"><![CDATA[Here is the Logo:

You have four choices:

[B&W .PDF|B&W .PDF|black & white PDF]

B&W .Tiff

[Color .PDF|^ESP logo color.pdf]

Color .Tiff
[Tiff image|^ESP logo color.tif]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">16220276</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">16253042</id>
<property name="body"><![CDATA[Here is the Logo:

You have four choices:

[B&W .PDF|B&W .PDF|black & white PDF]

B&W .Tiff

[Color .PDF|^ESP logo color.pdf]

[Color .Tiff|^ESP logo color.tif]]]></property>
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<property name="body"><![CDATA[h2. Engineering weekly meeting (Nov 29, 2007)

Present: Birch, Harris, Scholin, Everlove, Pargett, Roman&nbsp;

*Tech Transfer*
•&nbsp;&nbsp; &nbsp;Status of Bruce and Mack (and Moe)
•&nbsp;&nbsp; &nbsp;New hand construction update
•&nbsp;&nbsp; &nbsp;Status of new motors/ new motor brackets
•&nbsp;&nbsp; &nbsp;Cepheid coming Friday?

{color:#0033ff}Bruce and Mack are 97% assembled.&nbsp; Both lack hand, which only has slider issue to resolve, and all can be modified.&nbsp; Have ordered more blue nipples and tubing; should arrive end of this week (tomorrow?).&nbsp; 27 Maxon motors shipped yesterday.&nbsp; El Camino has not started machining new motor brackets because they lost our PO and the job fell out of que.&nbsp; Mike Parker will push to make them meet their original Dec. delivery date.{color}

{color:#0033ff}Cheri to order enough syringes to completely outfit Bruce, Mack, Moe, plus have a spare set.&nbsp; These are COTS.&nbsp; Scott still working to get custom, cold-rated syringes built.&nbsp; Break charge in thirds among 800560, 703506, 900612.{color}

{color:#0033ff}New motors to be placed on Bruce, Mack, and Moe; no changes to NEO and GG.&nbsp; Dwarf boards--we have enough for Moe, but then no extras.&nbsp; Must meet with Scott about new order.{color}

{color:#0033ff}Cepheid IS arriving for visit tomorrow, 10am.&nbsp;{color}

{color:#0033ff}Chris S. says NOPP proposal generating much interest in PCR module.&nbsp; Sandia, Stoneybrook, U Maine all have detection technologies they would like to use with our fluidics layout.&nbsp;&nbsp; We must clarify IP issues with LLNL about transfer of fluidics (not PCR) technology to other parties.&nbsp; Also will impact how many dwarves to order.&nbsp; Have requested letters of support from us for their NOPP proposals.&nbsp;&nbsp; WHOI is taking our specifications for syringe assembly for their in-situ flow cytometer.&nbsp; A similar tech transfer agreement can be made to these other institutions once IP with LLNL worked out.&nbsp; Don Kennedy here next Weds; Chris giving a tour with NEO in test-tank area.{color}

*MFB*

•&nbsp;&nbsp; &nbsp;Status of adding AIV and new ASV
•&nbsp;&nbsp; &nbsp;Mounting of solid-phase extraction hardware
•&nbsp;&nbsp; &nbsp;Status of new script development
•&nbsp;&nbsp; &nbsp;Heater block sent to LLNL
•&nbsp;&nbsp; &nbsp;Prediction for 12-21-07?

{color:#0033ff}ASV now mounted and Addie's pushing water through.&nbsp; AIV still waiting on mounting brackets from El Camino. Script written to control valves without AIV.&nbsp; SPE mounted and moving water.&nbsp; Heater is easy to control.&nbsp; Chris has rec'd 12 more small columns and 12 holders.&nbsp; Addie will get one to Mike Parker to build another heater.&nbsp; PCR heater sent back to LLNL on Tuesday (11-27) and FedEx has it arriving 11-28 at 9:01am.&nbsp; Still to hear from Tony if it arrived.&nbsp; Hope is to have SPE working by 12-21.&nbsp; Fluidics will be ready by tomorrow.&nbsp; Then it is biochemistry testing.{color}

{color:#0033ff}Must still develop decon script for the SPE column/tubing.&nbsp;{color}

*Software*
•&nbsp;&nbsp; &nbsp;Tracing the Ruby garbage error...
•&nbsp;&nbsp; &nbsp;Plan for low power processor visit
•&nbsp;&nbsp; &nbsp;Progress of Bob Herlien on MFB drivers?
•&nbsp;&nbsp; &nbsp;Progress of Rich Schramm on GUI?
•&nbsp;&nbsp; &nbsp;JIRA?

{color:#0033ff}Brent able to reproduce the error, but cannot identify where it is occurring. &nbsp; Took debugging scaffolding and ported to run on the core processor and now is able to reproduce the error in a repeatable spot.&nbsp; He knows the structure and block that's getting messed up; perhaps modifying C-debugger to run code slower...{color}

{color:#0033ff}Work this week/end at pushing pucks through and reproducing the error.&nbsp; If no progress by Monday, then work on creating a 'test case' that would allow sending to other developers, who would run this code without the need for hardware.{color}

{color:#0033ff}Low power CPU visit postponed, but decision to change to lower powered CPU will wait, as the market is already moving in that direction.&nbsp; With this 'job' off the table, Jim will visit with Wayne R. about his timeline in 2008.{color}

{color:#0033ff}Bob Herlien has PCR driver multi-threading finished and awaits hardware to test in on.{color}

{color:#0033ff}Rich Schramm pulled off ESP GUI development for 2 weeks for MARS work; we will get him in January.&nbsp; Plan is to use GUI during spring '08 deployment, which means we need it to fiddle with by \~March, '08.&nbsp;{color}

*Sphere and 4K DWSM*
•&nbsp;&nbsp; &nbsp;Ordering sphere
•&nbsp;&nbsp; &nbsp;Still awaiting machining quote from Hanard Machining, Oregon.
•&nbsp;&nbsp; &nbsp;DWSM---need for mechanical design (Doug's return?)]]></property>
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<property name="body"><![CDATA[Here is the Logo:\\ \\

You have four choices:

[B&W .PDF|B&W .PDF|black & white PDF]

B&W .Tiff

Color .PDF

Color .Tiff 
[Tiff image|^ESP logo color.tif]]]></property>
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<property name="body"><![CDATA[h2. Engineering weekly meeting (Nov 29, 2007)

Present: Birch, Harris, Scholin, Everlove, Pargett, Roman&nbsp;

*Tech Transfer*
•&nbsp;&nbsp; &nbsp;Status of Bruce and Mack (and Moe)
•&nbsp;&nbsp; &nbsp;New hand construction update
•&nbsp;&nbsp; &nbsp;Status of new motors/ new motor brackets
•&nbsp;&nbsp; &nbsp;Cepheid coming Friday?

{color:#0033ff}Bruce and Mack are 97% assembled.&nbsp; Both lack hand, which only has slider issue to resolve, and all can be modified.&nbsp; Have ordered more blue nipples and tubing; should arrive end of this week (tomorrow?).&nbsp; 27 Maxon motors shipped yesterday.&nbsp; El Camino has not started machining new motor brackets because they lost our PO and the job fell out of que.&nbsp; Mike Parker will push to make them meet their original Dec. delivery date.{color}

{color:#0033ff}Cheri to order enough syringes to completely outfit Bruce, Mack, Moe, plus have a spare set.&nbsp; These are COTS.&nbsp; Scott still working to get custom, cold-rated syringes built.&nbsp; Break charge in thirds among 800560, 703506, 900612.{color}

{color:#0033ff}New motors to be placed on Bruce, Mack, and Moe; no changes to NEO and GG.&nbsp; Dwarf boards--we have enough for Moe, but then no extras.&nbsp; Must meet with Scott about new order.{color}

{color:#0033ff}Cepheid IS arriving for visit tomorrow, 10am.&nbsp;{color}

{color:#0033ff}Chris S. says NOPP proposal generating much interest in PCR module.&nbsp; Sandia, Stoneybrook, U Maine all have detection technologies they would like to use with our fluidics layout.&nbsp;&nbsp; We must clarify IP issues with LLNL about transfer of fluidics (not PCR) technology to other parties.&nbsp; Also will impact how many dwarves to order.&nbsp; Have requested letters of support from us for their NOPP proposals.&nbsp;&nbsp; WHOI is taking our specifications for syringe assembly for their in-situ flow cytometer.&nbsp; A similar tech transfer agreement can be made to these other institutions once IP with LLNL worked out.&nbsp; Don Kennedy here next Weds; Chris giving a tour with NEO in test-tank area.{color}

*MFB*

•&nbsp;&nbsp; &nbsp;Status of adding AIV and new ASV
•&nbsp;&nbsp; &nbsp;Mounting of solid-phase extraction hardware
•&nbsp;&nbsp; &nbsp;Status of new script development
•&nbsp;&nbsp; &nbsp;Heater block sent to LLNL
•&nbsp;&nbsp; &nbsp;Prediction for 12-21-07?

{color:#0033ff}ASV now mounted and Addie's pushing water through.&nbsp; AIV still waiting on mounting brackets from El Camino. Script written to control valves without AIV.&nbsp; SPE mounted and moving water.&nbsp; Heater is easy to control.&nbsp; Chris has rec'd 12 more small columns and 12 holders.&nbsp; Addie will get these (2? 3? all?) to Mike Parker to build more heaters.&nbsp; PCR heater sent back to LLNL on Tuesday (11-27) and FedEx has it arriving 11-28 at 9:01am.&nbsp; Still to hear from Tony if it arrived.&nbsp; Hope is to have SPE working by 12-21.&nbsp; Fluidics will be ready by tomorrow.&nbsp; Then it is biochemistry testing.{color}

{color:#0033ff}Must still develop decon script for the SPE column/tubing.&nbsp;{color}

*Software*
•&nbsp;&nbsp; &nbsp;Tracing the Ruby garbage error...
•&nbsp;&nbsp; &nbsp;Plan for low power processor visit
•&nbsp;&nbsp; &nbsp;Progress of Bob Herlien on MFB drivers?
•&nbsp;&nbsp; &nbsp;Progress of Rich Schramm on GUI?
•&nbsp;&nbsp; &nbsp;JIRA?

*Sphere and 4K DWSM*
•&nbsp;&nbsp; &nbsp;Ordering sphere
•&nbsp;&nbsp; &nbsp;Still awaiting machining quote from Hanard Machining, Oregon.
•&nbsp;&nbsp; &nbsp;DWSM---need for mechanical design (Doug's return?)]]></property>
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<property name="body"><![CDATA[h2. Engineering weekly meeting (Nov 29, 2007)

Present: Birch, Harris, Scholin, Everlove, Pargett, Roman&nbsp;

*Tech Transfer*
•&nbsp;&nbsp; &nbsp;Status of Bruce and Mack (and Moe)
•&nbsp;&nbsp; &nbsp;New hand construction update
•&nbsp;&nbsp; &nbsp;Status of new motors/ new motor brackets
•&nbsp;&nbsp; &nbsp;Cepheid coming Friday?

{color:#0033ff}Bruce and Mack are 97% assembled.&nbsp; Both lack hand, which only has slider issue to resolve, and all can be modified.&nbsp; Have ordered more blue nipples and tubing; should arrive end of this week (tomorrow?).&nbsp; 27 Maxon motors shipped yesterday.&nbsp; El Camino has not started machining new motor brackets because they lost our PO and the job fell out of que.&nbsp; Mike Parker will push to make them meet their original Dec. delivery date.{color}

{color:#0033ff}Cheri to order enough syringes to completely outfit Bruce, Mack, Moe, plus have a spare set.&nbsp; These are COTS.&nbsp; Scott still working to get custom, cold-rated syringes built.&nbsp; Break charge in thirds among 800560, 703506, 900612.{color}

{color:#0033ff}New motors to be placed on Bruce, Mack, and Moe; no changes to NEO and GG.&nbsp; Dwarf boards--we have enough for Moe, but then no extras.&nbsp; Must meet with Scott about new order.{color}

{color:#0033ff}Cepheid IS arriving for visit tomorrow, 10am.&nbsp;{color}

{color:#0033ff}Chris S. says NOPP proposal generating much interest in PCR module.&nbsp; Sandia, Stoneybrook, U Maine all have detection technologies they would like to use with our fluidics layout.&nbsp;&nbsp; We must clarify IP issues with LLNL about transfer of fluidics (not PCR) technology to other parties.&nbsp; Also will impact how many dwarves to order.&nbsp; Have requested letters of support from us for their NOPP proposals.&nbsp;&nbsp; WHOI is taking our specifications for syringe assembly for their in-situ flow cytometer.&nbsp; A similar tech transfer agreement can be made to these other institutions once IP with LLNL worked out.&nbsp; Don Kennedy here next Weds; Chris giving a tour with NEO in test-tank area.{color}

*MFB*

•&nbsp;&nbsp; &nbsp;Status of adding AIV and new ASV
•&nbsp;&nbsp; &nbsp;Mounting of solid-phase extraction hardware
•&nbsp;&nbsp; &nbsp;Status of new script development
•&nbsp;&nbsp; &nbsp;Heater block sent to LLNL
•&nbsp;&nbsp; &nbsp;Prediction for 12-21-07?

ASV now mounted and Addie's pushing water through.&nbsp; AIV still waiting on mounting brackets from El Camino. Script written to control valves without AIV.&nbsp; SPE mounted and moving water.&nbsp; Heater is easy to control.&nbsp; Chris has rec'd 12 more small columns and 12 holders.&nbsp; Addie will get these (2? 3? all?) to Mike Parker to build more heaters.&nbsp; PCR heater sent back to LLNL on Tuesday (11-27) and FedEx has it arriving 11-28 at 9:01am.&nbsp; Still to hear from Tony if it arrived.&nbsp; Hope is to have SPE working by 12-21.&nbsp; Fluidics will be ready by tomorrow.&nbsp; Then it is biochemistry testing.

Must still develop decon script for the SPE column/tubing.&nbsp;

Software
•&nbsp;&nbsp; &nbsp;Tracing the Ruby garbage error...
•&nbsp;&nbsp; &nbsp;Plan for low power processor visit
•&nbsp;&nbsp; &nbsp;Progress of Bob Herlien on MFB drivers?
•&nbsp;&nbsp; &nbsp;Progress of Rich Schramm on GUI?
•&nbsp;&nbsp; &nbsp;JIRA?

Sphere and 4K DWSM
•&nbsp;&nbsp; &nbsp;Ordering sphere
•&nbsp;&nbsp; &nbsp;Still awaiting machining quote from Hanard Machining, Oregon.
•&nbsp;&nbsp; &nbsp;DWSM---need for mechanical design (Doug's return?)]]></property>
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<property name="body"><![CDATA[Here is the Logo:



You have four format choices:

[B&W .PDF|^ESP logo bw.PDF|b&w PDF]

[B&W .Tiff|^ESP logo bw.tif|b&w tiff]

[Color .PDF|^ESP logo color.pdf|color PDF]

[Color .TIF|^ESP logo color.tif|color TIFF]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">16220284</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">16253050</id>
<property name="body"><![CDATA[Here is the Logo: !ESP logo color.png|thumbnail!
&nbsp;You have four format choices:
[B&W .PDF|^ESP logo bw.PDF|b&w PDF]

[B&W .Tiff|^ESP logo bw.tif|b&w tiff]

[Color .PDF|^ESP logo color.pdf|color PDF]

[Color .TIF|^ESP logo color.tif|color TIFF]]]></property>
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</property>
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<id name="id">9831275</id>
<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 \- no meeting; first D-ESP deployment
# 30Apr2009 \- no meeting; final D-ESP deployment tomorrow
# [07May2009]]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.


Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.


Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew ? ]]></property>
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<property name="body"><![CDATA[Here is the Logo:

You have four choices:

[B&W .PDF|^B&W .PDF|black & white PDF]

[B&W .Tiff|^B&W logo]

[Color .PDF|^ESP logo color.pdf|color PDF]

[Color .TIF|^ESP logo color.tif|color TIFF]]]></property>
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<property name="body"><![CDATA[resent:&nbsp; Scott, Brent, Doug, Jim, Gene


Absent:&nbsp; Chris S., Cheri, Addie, Wayne

h3. Machine Builds


h3. MFB


h3. Drifter

* Pre-Flyer cruise dive days on the Zephyr have been pushed back to May 26 and May 27
* Gene will be in Test Tank Monday/Tuesday
* Ordering radar reflector.&nbsp; Have blinky light.&nbsp; PPP is running via wire.&nbsp; Scott will set-up Freewave's
* If time, will pull Iridium off an existing surface mooring and mount on Drifter.

h3. Software

* Brent's been working on HP pump.&nbsp; It seems to run either full on or off.&nbsp; Difficult to run it at other than 2000rpm.&nbsp; He has a was to work servo control with this constraint.
* Next is to characterize the differential pressure sensors then
* run sample fluid through the core loop
* Noticed that TSV seems to get off by 7-9 counts when you power cycle. Scott will watch while they try and re-create.
* Discussion about making the laptop on the boat a 'slave' to the shorestation, so missions can be started right on the boat (boat laptop--> shore station-->ESP buoy) instead of having to rely on someone on the shore.

h3. Deep ESP


h6.

* Will talk to Science about needs for a metal wand to withstand high temperatures at Axial.&nbsp; Otherwise, with current design, the end of the 'wand' is actually a solenoid valve.
* Doug showed valve design to Brent and explained function.
* Must get Science buy-in about wand idea, but in the meantime we will push forward with this design.

h3. GUI


h3. Deployment Issues

* Two potential sites to visit in June:
* \#1.&nbsp; 2900m \[36.61N, 122.44W\].&nbsp; Flat, open, clear water.&nbsp; Nearby clam-field.
* \#2.&nbsp; 1800m \[36.71N, 122.1W\].&nbsp; Flat, poorer visibility.&nbsp; very old whale-fall.
* Much discussion of which site.&nbsp; Consensus was that August cruise is most critical (depths of 1400-1600m), thus site #2 would provide adequate testing for August without undue risk.&nbsp;&nbsp;
* A very rough deployment schedule was discussed.&nbsp; Leave MBARI @ 11am on Friday, June 5, return Tuesday, June 9.&nbsp; Chris and I will meet with ship crew 10am (Tank View) Tuesday to discuss.
* 4K ISUS mtg Tuesday @ 11--Tank View.&nbsp; Will meet with Luke, John R., and science.

h3. Other Items:]]></property>
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<property name="body"><![CDATA[Here is the Logo:

You have four choices:

[B&W .PDF|^ESP logo bw.PDF|black & white PDF]

[B&W .Tiff|^ESP logo bw.tif|b&w tiff]

[Color .PDF|^ESP logo color.pdf|color PDF]

[Color .TIF|^ESP logo color.tif|color TIFF]]]></property>
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</property>
</object>
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<id name="id">16253055</id>
<property name="body"><![CDATA[Here is the Logo: !ESP logo color.png|thumbnail!

h2. Below are some high-resolutions formats you may like:

[B&W .PDF|^ESP logo bw.PDF|b&w PDF]

[B&W .TIFF|^ESP logo bw.tif|b&w tiff]

[Color .PDF|^ESP logo color.pdf|color PDF]

[Color .TIFF|^ESP logo color.tif|color TIFF]]]></property>
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</property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">16253051</id>
<property name="body"><![CDATA[Here is the Logo: !ESP logo color.png|thumbnail!

h2. Below are some high-resolutions formats you may like:


[B&W .PDF|^ESP logo bw.PDF|b&w PDF]

[B&W .Tiff|^ESP logo bw.tif|b&w tiff]

[Color .PDF|^ESP logo color.pdf|color PDF]

[Color .TIF|^ESP logo color.tif|color TIFF]]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|ESP Automated Image Analysis]

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter 
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size. 
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|ESP Automated Image Analysis]

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter 
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size. 
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h3. [ESP Logos]


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010]]></property>
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<property name="body"><![CDATA[h2. *ESP Engineering weekly mtg (11-15-2007)*

Present: Jensen, Scholin, Everlove, Birch, Harris

*Tech Transfer*
•&nbsp;&nbsp;&nbsp; Still on track to have 2 instruments wired & plumbed by Thanksgiving?
2 units almost completely wired (boards/valves/motors).&nbsp; End of day both powered.&nbsp; Plumbing parts in yesterday and will continue this afternoon.&nbsp; Do 2 units first then retrofit Neo.

•&nbsp;&nbsp;&nbsp; Hand/puck sticking issue?&nbsp; (still working on)&nbsp; New hand design?(getting close, tackled pivot-point and the cam,&nbsp; but still figuring how to support forearm pulley so belt can be fully loaded)

•&nbsp;&nbsp;&nbsp; Science getting to use yet?
Using GG. Don't need Neo

•&nbsp;&nbsp;&nbsp; Time for delivery of new motors/brackets?
Still waiting on brackets (Mike supposed ot have sent PO to El Camino yesterday) and motors (due end Nov).

•&nbsp;&nbsp;&nbsp; Other issues

If some grants come in, we will have many instruments needed around the country.&nbsp; Chris is pushing for building all three (don't leave one as parts).&nbsp; In the near future we will need another production run and should keep in mind parts for the future.

*Software*
•&nbsp;&nbsp;&nbsp; Progress in Tracing of log comments?
•&nbsp;&nbsp;&nbsp; Bob Herlien progress on MFB drivers?
•&nbsp;&nbsp;&nbsp; Rich Schramm progress on GUI?
•&nbsp;&nbsp;&nbsp; JIRA implementation
Discussion of these items tabled since Brent is gone.

*MFB*
•&nbsp;&nbsp;&nbsp; Results from Tues/Weds and subsequent plan going forward
•&nbsp;&nbsp;&nbsp; Solid-Phase-Extraction status
•&nbsp;&nbsp;&nbsp; CAV (AIV) valve arrival?
•&nbsp;&nbsp;&nbsp; Overall parts inventory; do we have everything we need?

Building slug on bench then pulling through the ARV and running in the MFB heater and collecting it after and looking at peak fluorescence and run on gel.&nbsp; WE HAVE AMPLIFICATION.&nbsp; Solutions seems to be due to better cleanliness and care in handling reagents.&nbsp; Optics within the LLNL heater block do not appear to be working properly.&nbsp; Today will actually _build_ the slug from the ARV and then repeat yesterday's successful procedure.&nbsp; If successful, will add ATV and repeat.&nbsp; Chris P. has ordered more fluorescent dye.&nbsp; When it arrives we will do a final test of the optics ourselves before we (most likely) must send the block back to LLNL.

*4K issues*
•&nbsp;&nbsp;&nbsp; Quotes for casting the 4K sphere are here: [Wah Chang|^Wah Chang quote MBARI 60200 11-14 C5.pdf] and the quote for machining it are here: [Tapemation|^Tapemation quote MBARI 4K Hemi.doc]
•&nbsp;&nbsp;&nbsp; BOM for sphere, fittings, elevator, all accessories

Other issues
&nbsp;]]></property>
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<property name="body"><![CDATA[h2. *ESP Engineering weekly mtg (11-15-2007)*

Present: Jensen, Scholin, Everlove, Birch, Harris

*Tech Transfer*
•&nbsp;&nbsp;&nbsp; Still on track to have 2 instruments wired & plumbed by Thanksgiving?
2 units almost completely wired (boards/valves/motors).&nbsp; End of day both powered.&nbsp; Plumbing parts in yesterday and will continue this afternoon.&nbsp; Do 2 units first then retrofit Neo.

•&nbsp;&nbsp;&nbsp; Hand/puck sticking issue?&nbsp; (still working on)&nbsp; New hand design?(getting close, tackled pivot-point and the cam,&nbsp; but still figuring how to support forearm pulley so belt can be fully loaded)

•&nbsp;&nbsp;&nbsp; Science getting to use yet?
Using GG. Don't need Neo

•&nbsp;&nbsp;&nbsp; Time for delivery of new motors/brackets?
Still waiting on brackets (Mike supposed ot have sent PO to El Camino yesterday) and motors (due end Nov).

•&nbsp;&nbsp;&nbsp; Other issues

If some grants come in, we will have many instruments needed around the country.&nbsp; Chris is pushing for building all three (don't leave one as parts).&nbsp; In the near future we will need another production run and should keep in mind parts for the future.

*Software*
•&nbsp;&nbsp;&nbsp; Progress in Tracing of log comments?
•&nbsp;&nbsp;&nbsp; Bob Herlien progress on MFB drivers?
•&nbsp;&nbsp;&nbsp; Rich Schramm progress on GUI?
•&nbsp;&nbsp;&nbsp; JIRA implementation
Discussion of these items tabled since Brent is gone.

*MFB*
•&nbsp;&nbsp;&nbsp; Results from Tues/Weds and subsequent plan going forward
•&nbsp;&nbsp;&nbsp; Solid-Phase-Extraction status
•&nbsp;&nbsp;&nbsp; CAV (AIV) valve arrival?
•&nbsp;&nbsp;&nbsp; Overall parts inventory; do we have everything we need?

Building slug on bench then pulling through the ARV and running in the MFB heater and collecting it after and looking at peak fluorescence and run on gel.&nbsp; WE HAVE AMPLIFICATION.&nbsp; Solutions seems to be due to better cleanliness and care in handling reagents.&nbsp; Optics within the LLNL heater block do not appear to be working properly.&nbsp; Today will actually _build_ the slug from the ARV and then repeat yesterday's successful procedure.&nbsp; If successful, will add ATV and repeat.&nbsp; Chris P. has ordered more fluorescent dye.&nbsp; When it arrives we will do a final test of the optics ourselves before we (most likely) must send the block back to LLNL.

*4K issues*
•&nbsp;&nbsp;&nbsp; Sphere plans to Wah Chang and Tapemation
•&nbsp;&nbsp;&nbsp; BOM for sphere, fittings, elevator, all accessories



Other issues
&nbsp;]]></property>
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Present:]]></property>
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# [Meeting Notes from June 7, 2007|http://oceana.shore.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc]
\\

Meeting minutes stored within Confluence:
# [08nov2007]
# [15Nov2007]
# [Proprietary notes]]]></property>
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h3. Administrative

# [2007 Meeting Notes]

h3. Engineering

# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
h4. Software Issues
# [JIRA Bug Tracker]

h3. Science]]></property>
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# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Micro-Fluidics Block]
# [2007 Meeting Notes]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]]]></property>
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# [GUI Component Development Pages|2G ESP GUI Project Page]
# Micro-Fluidics Block
# [2007 Meeting Notes]]]></property>
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<property name="body"><![CDATA[*ESP Engineering weekly mtg (11-11-07)*


Present: Brent Roman, Addie Harris, Scott Jensen, Cheri Everlove, Jim Birch

&nbsp;Tech Transfer: Build of 2 new instruments moving along smoothly.&nbsp; New motor brackets being sent to El Camino for machining.&nbsp; That charge (~$3500) must be subdivided b/w various accounts.&nbsp; Wait to talk to Scholin about this.&nbsp; By Thanksgiving, both machines should be wired and plumbed.

Much discussion about puck sticking to O-ring, and possible fixes/re-designs.&nbsp; Scott looking into.

&nbsp;Software:&nbsp; Ported our code from v1.6.8 up to 1.8.6 and (unfortunately) found exactly the same errors at the same spot.&nbsp; Cannot be made to fail on the simulator, but fails on the actual instrument.&nbsp; Brent attacking this by tracing log comments.&nbsp; Brent attended Ruby Conference in Charlotte, NC and is interested in J-Ruby for our shore station. Will look into.

&nbsp;MFB:&nbsp; still not working but Chris and Addie have run a large number of experiments to try and isolate where our reagent mix is being 'killed'.&nbsp; Conclusion so far is that something within the fluidics block is inhibiting the reaction, since building slugs from the block show diminishing PCR activity the longer we wait to run on the 7700.&nbsp; Trying to build slugs only going through ARV, and other permutations to see where the contamination is entering.

&nbsp;Vacations discussed.&nbsp; Brent will be away for most of Dec.&nbsp; All others have short holiday vacations planned.

Discussion about starting to keep notes on Confluences, this record being the first.&nbsp; Question came up about how easy it would be to search Confluence records.&nbsp;\\]]></property>
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# [Meeting Notes from June 7, 2007|http://oceana.shore.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc]
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<property name="body"><![CDATA[h2. Overview of ESP Image Analysis Automation

# [Investigations into Automated Image Analysis]
# [Extracting GAL Point Features]
# [Extracting Image Point Features]
# [Extracting Image Fiducial Features]
# [Point Feature Alignment]

h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]]]></property>
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# [Meeting Notes from June 7, 2007|http://oceana.shore.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc]
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<property name="body"><![CDATA[h4. {color:#ff00cc}MAKAI flight w 4 Archives, 1 Lyse-n-go{color}

*Feb 2-4, 2016*

Repeat of Dec flight.&nbsp; Here are notes from Yanwu's summary:

(Note: when reaching each target depth (peak-chl or pre-set), we give Makai 10 minutes to damp down depth undulation.)

Sample#1 (lyse&go sample. At chl peak):
Makai descended from surface, found the chl peak at 8.7m. On the ensuing ascent, Makai held depth at 8.7m, and triggered sample#1.
Took 63 minutes to complete.&nbsp; Then Makai surfaced to "report to shore".

Sample#2 (archive sample. At chl peak):
Makai descended from surface, found the chl peak at 12.7m. On the ensuing ascent, Makai held depth at 12.3m, and triggered sample#2. (Note: the water column was quite mixed vertically. The chl values at 8m and 12m were very close. Makai was doing her best to pick the relatively weak peak.)&nbsp; Took 41 minutes to complete.

Sample#3 (archive sample. At reacquired chl peak):
In order to reacquire the chl peak (considering the peak-chl layer may have moved up or down), Makai intentionally wiggled up and down (up first, then down, and then up). On the "down", it found the chl peak at 13.2m. On the ensuing "up", Makai held depth at 13.0m, and triggered sample#3.&nbsp; Took 40 minutes to complete.

Sample#4 (archive sample. At pre-set 27m. Control sample.):
Makai dove to the pre-set 27m depth, and triggered sample#4.&nbsp; Took 39 minutes to complete.

Sample#5 (archive sample. At pre-set 27m. Control sample.):
Makai stayed at the pre-set 27m depth, and triggered sample#5.&nbsp; Took 38 minutes to complete.

h4. {color:#ff00cc}Del Mar--ESP-Waldo{color}

*May 17, 2016*

Used M/V Merlin (Walt Crampton), with MBARI surface mooring.&nbsp; Divers from SCRIPPS.&nbsp; Deployed with CTD about 400 yds from Del Mar mooring (SE of their mooring). Used new anchor line, #1 shockle, and 35m EM cable.

Ship coordinates when we dropped it:&nbsp; 32' 55.603N&nbsp; 117' 18.895W
Melo coordinates (IMEI: 300034012090780):&nbsp; 32.92633 \-117.31491

Water depth 100m.&nbsp; Divers reported master link at 22.8m, can top at 16.76m.&nbsp; CTD reading \~18m.

Initial mission is to take a sample two hours after sunrise, every weekday.

*Nov 10, 2016*

Recovered ESP-Waldo.&nbsp; used M/V Merlin with Scripps divers.&nbsp; Drove home with 5'x9' trailer w/ramp using MBARI van #4.


h4.


h4. {color:#ff00cc}ESP-Moe;&nbsp; Moran in Monterey Bay{color}

*Sep 26, 2016*

After two-day wait for weather to settle, deployed ESP MOE at M0.&nbsp; No  mission loaded, as they wanted to manually fire each archive and have  more control over when they would manually collect samples.

Shana Rae used, with Charles Bock & Mike Conway diving.&nbsp; 15.6m EM cable with Shockle #2.&nbsp; CTD is around 5.65m deep.

Oct 7, lost comms to Moe.&nbsp; Modem and Cell provider check out.&nbsp;  Electrical signal up/down EM cable check out.&nbsp; Oct 11 bring out computer  to see if we can talk to can.&nbsp; no luck.


&nbsp;*Oct 13, 2016*

&nbsp;Got Shana Rae and divers (Eric + George) at the last minute.&nbsp; Weather beautiful. Flat.&nbsp; Recovered instrument on deck, and tried three ways to tunnel in to talk to host.&nbsp; No luck.&nbsp; Brought instrument home and could not communicate with host after uncanning.&nbsp; Scott traded carrier board with one in Brent's office and it worked.&nbsp; Moe carrier board did not work on another Sleepy.&nbsp; Work continues to discover why/ what went wrong on carrier board.

&nbsp;*Oct 27, 2016*

&nbsp;Got Shana Rae and divers (Jeff S and Paul C.).&nbsp;  Deployment went very smoothly.&nbsp; difficult cell phone reception at site.&nbsp; Got confirmation of depth (6.7m) and started home.&nbsp; After about 15 minutes got call from Brent that carousel was jammed and would not turn.&nbsp; Suggested recover.&nbsp; We returned and recovered and brought everything home.&nbsp; inspection showed that a carousel rod had unscrewed itself,fallen, and jammed against the elevator, freezing the carousel.&nbsp; Weather is turning more mercurial; will try to redeploy on Wed, Nov 2.
\\

*Nov 2, 2016* &nbsp;

Got Shana Rae and divers (Jeff S and Mike C).&nbsp; Deployment went smoothly, although had to wait for fueling of WF on dock.&nbsp; Left 11:30am, returned \~3pm.&nbsp; Depth 6.5m.&nbsp; This will be a 2-week run.

*Nov 17, 2016*

Textbook recovery of ESP-Moe, ending the Moran deployment.&nbsp; Used Shana Rae w/ divers, George & Kim R.&nbsp; Left dock at 8:20am, returned \~11:00.&nbsp; Some swell and coolish/cold. ]]></property>
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<id name="id">2195653</id>
<property name="body"><![CDATA[Meeting minutes stored in the projectlibrary:&nbsp;
# [Meeting Notes from June 7, 2007|http://oceana.shore.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc]
\\

Meeting minutes stored within Confluence:]]></property>
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<property name="body"><![CDATA[h2. Extracting _Spots_ from ESP Images

The spots extracted from the image are used to calculate the fitness of the match between the GAL file and image file. 

h1. The Short Version
The first step is to read the raw tiff image:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = imageIOService.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}
!Extracting Image Fiducial Features^pcr11jun2520h2000ml40s.png!

There is a small function call that extracts the image spots. 
{code}
import org.mbari.esp.ia.imglib.MultiPassRegionsExtractorFn
val regions = MultiPassRegionsExtractorFn(image)
val points = regions.map(_.centroid).toSeq
{code}
The above code snippet does the following:
# Extracts the bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{regions.map(_.centroid).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of points is then converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val circles = points.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("pcr11jun2520h2000ml40ss-with-extracted-spots.png"))
g2.dispose()
{code}
!pcr11jun2520h2000ml40ss-with-extracted-spots.png!

h1. Under the Hood

In order to extract the regions that represent the spots we threshold at multiple levels using 2 different image treatments. The 2 image treatments are:
# Raw (no treatment)
# Standard deviation of image using a local 3x3 kernel.

We calculate a base threshold for each treatment using _maximum entropy_. Then we make multiple passes across the image from using the following:
{code}
val bound = 25 // Add and subtract this from threshold to get range
val minVal = if (split - bound < 0) split else split - bound
val maxVal = if (split + bound > 255) split else split + bound
for (i <-  minVal to maxVal by 5) {
    // Process image. ie. apply threshold and floodfill
}
{code}

For each pass across an image, we aggregate all the regions into a collection. During the aggregations we eliminate spurious or duplicate regions by:
# Exclude non-round regions. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest (e.g. {{filter(_.eccentricity()._1 < 3)}})
# Exclude regions that contain less than 10 pixels. 
# Exclude regions whose centroid duplicates an existing accepted region. (i.e. {{c1.x == c2.x && c1.y == c2.y}})
# Drop regions whose centroid is within 3 pixels of another region. These are likely to be regions that represent the same spot.


[Extracting Image Point Features 2]]]></property>
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<property name="body"><![CDATA[h2. Extracting _Spots_ from ESP Images

The spots extracted from the image are used to calculate the fitness of the match between the GAL file and image file. 

h1. The Short Version
The first step is to read the raw tiff image:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = io.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}
!Extracting Image Fiducial Features^pcr11jun2520h2000ml40s.png!

There is a small function call that extracts the image spots. 
{code}
import org.mbari.esp.ia.imglib.MultiPassRegionsExtractorFn
val regions = MultiPassRegionsExtractorFn(image)
val points = regions.map(_.centroid).toSeq
{code}
The above code snippet does the following:
# Extracts the bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{regions.map(_.centroid).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of points is then converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val circles = points.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("pcr11jun2520h2000ml40ss-with-extracted-spots.png"))
g2.dispose()
{code}
!pcr11jun2520h2000ml40ss-with-extracted-spots.png!

h1. Under the Hood

In order to extract the regions that represent the spots we threshold at multiple levels using 2 different image treatments. The 2 image treatments are:
# Raw (no treatment)
# Standard deviation of image using a local 3x3 kernel.

We calculate a base threshold for each treatment using _maximum entropy_. Then we make multiple passes across the image from using the following:
{code}
val bound = 25 // Add and subtract this from threshold to get range
val minVal = if (split - bound < 0) split else split - bound
val maxVal = if (split + bound > 255) split else split + bound
for (i <-  minVal to maxVal by 5) {
    // Process image. ie. apply threshold and floodfill
}
{code}

For each pass across an image, we aggregate all the regions into a collection. During the aggregations we eliminate spurious or duplicate regions by:
# Exclude non-round regions. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest (e.g. {{filter(_.eccentricity()._1 < 3)}})
# Exclude regions that contain less than 10 pixels. 
# Exclude regions whose centroid duplicates an existing accepted region. (i.e. {{c1.x == c2.x && c1.y == c2.y}})
# Drop regions whose centroid is within 3 pixels of another region. These are likely to be regions that represent the same spot.


[Extracting Image Point Features 2]]]></property>
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<property name="body"><![CDATA[Meeting minutes stored in the projectlibrary:&nbsp;

# [Meeting Notes from June 7, 2007|http://oceana.shore.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc]
]]></property>
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<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = imageIOService.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}

!pcr11jun2520h2000ml40s.png!

h2. Extracting Bright Spots

The fiducials are typically the brightest areas on the image, especially in contrast to pixels immediately adjacent to the fiducial spots. We take advantage of this quality and isolate the fiducials by calculating the standard deviation of a 3x3 kernel across the entire image. The reason is clearly evident when looking at a surface plot of the raw image vs. the standard deviation. On the raw image, the fiducials may not be distinct from noisy backgrounds. However, when when using the standard deviation the fiducials sharply contrast with the rest of the image. In the images below, the 3 brightest peaks are the fiducial spots on the image.

!rawimage.png|width=900!
!stdimage.png|width=900!

We can extract the bright regions with the following code:
{code}
import org.mbari.esp.ia.imglib.BrightSpotExtractorFn
val regions = BrightSpotExtractorFn(rawImage)
{code}

{info:title:BrightSpotExtractorFn}
The internals of this function use a very standard pattern for spot extraction. The steps boil down to:
# Convert the image to 8-bit Gray so that we can calculate the histogram very quickly.
# Threshold the image using _maximum entropy_. _Renyi's entropy_ also works well but takes longer to calculate.
# Convert the binary threhold image to 16-bit *before* flood filling. Sometimes there is more than 256 regions, which can not be represented in an 8-bit image.
# Remove the area outside of a central circle. In general, we use a circle radius of 75% of the minimum radius of an image.
# Flood fill the image. Regions with less than 5 pixels are considered to be noise and are ignored.

Here's the function in it's entirety:
{code}
package org.mbari.esp.ia.imglib

import ij.process.ImageProcessor
import org.mbari.esp.ia.awt.ShortRegion

object BrightSpotExtractorFn extends (ImageProcessor => Iterable[ShortRegion]) {

    def apply(from: ImageProcessor): Iterable[ShortRegion] = {
        // Calculate local standard deviation for every 3x3 block of pixels
        val to = StdFn(from)

        val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
        val floodFill = {
            val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
            val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
            To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
        }
        val fill = threshold andThen floodFill

        SpotRegionsFn(from, fill(to))

    }
}

{code}
{info}

Then draw the image as follows:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val points = regions.map(_.centroid)
val circles = points.map(p => new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))

val colorImage = ToRGBFn(image).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
io.write(colorImage, new File("pcr11jun2520h2000ml40s-with-extracted-fiducials.png"))
g2.dispose()
{code}

!pcr11jun2520h2000ml40s-with-extracted-fiducials.png!]]></property>
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<id name="id">19071719</id>
<property name="body"><![CDATA[h2. Extracting _Spots_ from ESP Images

The spots extracted from the image are used to calculate the fitness of the match between the GAL file and image file. 

h1. The Short Version
The first step is to read the raw tiff image:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = io.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}
!Extracting Image Fiducial Features^pcr11jun2520h2000ml40s.png!

There is a small function call that extracts the image spots. 
{code}
import org.mbari.esp.ia.imglib.MultiPassRegionsExtractorFn
val regions = MultiPassRegionsExtractorFn(image)
val points = regions.map(_.centroid).toSeq
{code}
The above code snippet does the following:
# Extracts the bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{regions.map(_.centroid).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of points is then converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val circles = points.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
io.write(colorImage, new File("pcr11jun2520h2000ml40ss-with-extracted-spots.png"))
g2.dispose()
{code}
!pcr11jun2520h2000ml40ss-with-extracted-spots.png!

h1. Under the Hood

In order to extract the regions that represent the spots we threshold at multiple levels using 2 different image treatments. The 2 image treatments are:
# Raw (no treatment)
# Standard deviation of image using a local 3x3 kernel.

We calculate a base threshold for each treatment using _maximum entropy_. Then we make multiple passes across the image from using the following:
{code}
val bound = 25 // Add and subtract this from threshold to get range
val minVal = if (split - bound < 0) split else split - bound
val maxVal = if (split + bound > 255) split else split + bound
for (i <-  minVal to maxVal by 5) {
    // Process image. ie. apply threshold and floodfill
}
{code}

For each pass across an image, we aggregate all the regions into a collection. During the aggregations we eliminate spurious or duplicate regions by:
# Exclude non-round regions. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest (e.g. {{filter(_.eccentricity()._1 < 3)}})
# Exclude regions that contain less than 10 pixels. 
# Exclude regions whose centroid duplicates an existing accepted region. (i.e. {{c1.x == c2.x && c1.y == c2.y}})
# Drop regions whose centroid is within 3 pixels of another region. These are likely to be regions that represent the same spot.


[Extracting Image Point Features 2]]]></property>
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<property name="body"><![CDATA[h4. (as of April, 2015)


h1. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).
* del mar 6 month (summer 2016)

*25.5m*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

*21.5m (BAD)*
Now with bad connector...&nbsp;
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos in the attachments of this page.
* late-2014; was this EM cable repaired?

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)
* Moran deployment (Sept/Oct 2016)

*15.2m (BAD; bad BSR?)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]

\\

All shockles modified Dec 2015 to be like 001 (stretchier cords)

h4. ESP-001 (modified with 'stretchier' cord)

* 44 days during Catalina (April 2014) deployment
* Moran MB deployment (Sep/Oct 2014)
* ECOHAB?
* Del Mar (start May 17, 2016)

h4. ESP-002

* Moran (sep/oct 2016)

h4. ESP-003


h4. ESP-004


h4. ESP-005


h1. Anchor lines

\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4. *57M*

* 2014 Moran deployment in MB
* moran (sep/oct 2016)

h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\
\\]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram11-19-07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]
# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.12|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.1%202%2011_19_2007.doc]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. The basic algorithm works as follows:

h1. The Alignment Algorithm

h2. The Basics

The basic building block of algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

Why use a chromosome to represent the points? Originally, feature alignement was done using a genetic algorithm, but it's been refined so that we now use some considerable less complex. 

The goal of our feature alignment is to find a non-rigid transform that rotates, scales and translates the gal points in euclidean space to align with point features extracted from the image. The recipe for this has several steps:
# [Read the GAL file and extract points for a single filter|Extracting GAL Point Features]
# Extract the fiducial points from the single fitler's gal points.
# [Read an ESP image and extract the bright fiducial spots|Extracting Image Fiducial Features]
# Read an ESP iamge and extract all spot features.
# Run through all the possible permutations of aligning the gal points to the image fiducial points
## Calculate the fitness for each permutation
## Select the _fittest_ alignment.



The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [linear transform|https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala] needed to rotate, scale, and align the GAL to the image and apply this to all the points in the GAL file.
# Calculate a fitness for the match between the image and GAL points. This fitness is actually a mutlipart evalucation
## First check that all the transformed GAL points are within the bounds of the image. If they are not we evaluate this match as _unfit_.
## Second, we check that the GAL points have not collapsed by calculating the most common distance between nearest neighbors. Then we check to see that this distance less than the maximum distance between image point pairs and greater then the minimum distance between point pairs.
## Finally, we use a weighted distance function. This calculates 
### the distance between all image points and all gal points. 
### Selects the GAL point nearest each image point.
### Takes the _distance_ parameter (we're using 7 pixels) and if the GAL-Image point distance is less than our distance param, we use the following {noformat}f  = fitness
d  = maximum distance [provided by user]
n  = number of image points
dn = distance from image point to nearest GAL point{noformat}
!fitnessfn.gif!]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]

h3. Engineering

# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
h4. Software Issues
# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]

h3. Science]]></property>
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<id name="id">2195711</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage |http://oceana.shore.mbari.org/ProjectLibrary/ESP/SURF%20Center/ESPLaborUsage.xls]

h3. Engineering

# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
h4. Software Issues
# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]

h3. Science]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">2195700</id>
<property name="body"><![CDATA[# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram11-19-07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">2162935</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">2195699</id>
<property name="body"><![CDATA[# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram11-19-07.ppt]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">2162934</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">2195701</id>
<property name="body"><![CDATA[# [Fluidics Tubing Diagram|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram11-19-07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]
# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.12|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.1%202%2011_19_2007.doc]]]></property>
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<property name="body"><![CDATA[h2. Extracting _Spots_ from ESP Images

h1. The Short Version
The first step is to read the raw tiff image:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = imageIOService.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}
!Extracting Image Fiducial Features^pcr11jun2520h2000ml40s.png!

There is a small function call that extracts the image spots. 
{code}
import org.mbari.esp.ia.imglib.MultiPassRegionsExtractorFn
val regions = MultiPassRegionsExtractorFn(image)
val points = regions.map(_.centroid).toSeq
{code}
The above code snippet does the following:
# Extracts the bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{regions.map(_.centroid).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of points is then converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val circles = points.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("pcr11jun2520h2000ml40ss-with-extracted-spots.png"))
g2.dispose()
{code}
!pcr11jun2520h2000ml40ss-with-extracted-spots.png!

h1. Under the Hood


# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h2. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h2. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn

// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutoContrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(acImage)).filter(_.eccentricity()._1 < 3)
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-ac-spots.png!

h2. Third Pass: Dynamic Contrast (Fuzzy-Sets)
{code}
import org.mbari.esp.ia.imglib.FuzzyContrastFn
val fuzzyContrastFn = To16BitGrayFn andThen FuzzyContrastFn
val fcImage = fuzzyContrastFn(rawImage)
val fcRegions = SpotRegionsFn(rawImage, rawFloodFill(fcImage)).filter(_.eccentricity()._1 < 3)
val fcPoints = fcRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(fcImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = fcPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-fc-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-fc-spots.png!

[Extracting Image Point Features 2]]]></property>
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<property name="body"><![CDATA[h2. Extracting _Spots_ from ESP Images

h1. The Short Version
The first step is to read the raw tiff image:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = imageIOService.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}
!Extracting Image Fiducial Features^pcr11jun2520h2000ml40s.png!

There is a small function call that extracts the image spots. 
{code}
import org.mbari.esp.ia.imglib.MultiPassRegionsExtractorFn
val regions = MultiPassRegionsExtractorFn(image)
val points = regions.map(_.centroid).toSeq
{code}
The above code snippet does the following:
# Extracts the bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{regions.map(_.centroid).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of points is then converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val circles = points.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("pcr11jun2520h2000ml40ss-with-extracted-spots.png"))
g2.dispose()
{code}
!pcr11jun2520h2000ml40ss-with-extracted-spots.png!

h1. Under the Hood

In order to extract the regions that represent the spots we threshold at multiple levels using 2 different image treatments. The 2 image treatments are:
# Raw (no treatment)
# Standard deviation of image using a local 3x3 kernel.

We calculate a base threshold for each treatment using _maximum entropy_. Then we make multiple passes across the image from using the following:
{code}
val bound = 25 // Add and subtract this from threshold to get range
val minVal = if (split - bound < 0) split else split - bound
val maxVal = if (split + bound > 255) split else split + bound
for (i <-  minVal to maxVal by 5) {
    // Process image. ie. apply threshold and floodfill
}
{code}

For each pass across an image, we aggregate all the regions into a collection. During the aggregations we eliminate spurious or duplicate regions by:
# Exclude non-round regions. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest (e.g. {{filter(_.eccentricity()._1 < 3)}} )
# Exclude regions that contain less than 10 pixels. 


[Extracting Image Point Features 2]]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Scott, Brent, Doug, Chris S, Jim, Gene, Kevin

Absent:&nbsp; Cheri, Addie, Wayne

h3. Machine Builds

* Harmonic drives in and Cheri working on switching them out
* McLane making progress on MFB's after I2C issue last week.
* h3. MFB

* \#1 is on NEO.&nbsp; #3 is on Moe.&nbsp; Just Received #4.&nbsp; All are running firmware version 4.03.&nbsp; Also rec'd our fourth module (labeled #5).
* Tony Makarewicz leaving LLNL tomorrow, May 8.

h3. Drifter

* May 13 dive day moved to October; First drifter dive is Monday, May 18. it will consist of Chris S., Gene, Scott, Jim.
* will use the E/M cable, but with a sealed end and a RR rail piece as the weight.
* Code is still in rudimentary stage.&nbsp; Gene would like someone to ask Linux/ C+\+ questions of if he needs.&nbsp; Kevin/Danelle/Brian K were volunteered.
* Hope to get in test tank by end of next week.
* Chris S. will fill out pre-cruise
* ppp connection has not been worked on for a week.&nbsp; Brent will provide Pete with cheat sheet and freewave manual to help him get started on the configuration.

h3. Software

* Gordon will NOT get modified ethernet driver.&nbsp; Deployments will not be long enough to warrant the power savings by changing the hub in the sphere, and Wayne is not here to help with the driver change.
* Code currently resides on Neo branch, Main branch, and GUI branch.&nbsp; Much disucssion on when to merge;&nbsp; on Gordon in lab tests we'll use GUI branch.&nbsp; {color:#ff0000}After June cruise we will merge GUI line with main line and run checkout on Gordon then{color}.
* Wireless comms.&nbsp; Decision is to use Freewave's to communicate wirelessly with the sphere.&nbsp; This requires a MINK connector/fitting; Scott will scrounge up/buy.

h3. Deep ESP


h6.

* Wand/valve tree.&nbsp; Doug can only get SS valves.&nbsp; He using some that Cheri has.&nbsp; They need minor modifications to be oil-compensated.
* Cables for valve tree have been ordered; should be here in 2 weeks
* 50' of cable for wand delivery
* Some discussion of tubing needed for wand, but a McMaster item so little lead-time.
* Wand stand still to be designed.&nbsp; Most likely will be something like a microphone stand.
* Doug has plans for a sectional bumper design for Oregon cruise.
* DWSM restarted and all switches worked.&nbsp; Doug and Brent to meet after to find out what might have gone wrong.

h3. GUI


h3. Deployment Issues.



h3. Other Items:

Jim in late Monday; picking up TWIC card.]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|Investigations into Automated Image Analysis].

I'm working on a new method. Documentation is [here|ESP Automated Image Analysis 2]

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter 
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size. 
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



]]></property>
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<property name="body"><![CDATA[h2. Extracting _Spots_ from ESP Images

h1. The Short Version
The first step is to read the raw tiff image:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = imageIOService.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}
!Extracting Image Fiducial Features^pcr11jun2520h2000ml40s.png!

There is a small function call that extracts the image spots. 
{code}
import org.mbari.esp.ia.imglib.MultiPassRegionsExtractorFn
val regions = MultiPassRegionsExtractorFn(image)
val points = regions.map(_.centroid).toSeq
{code}
The above code snippet does the following:
# Extracts the bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{regions.map(_.centroid).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of points is then converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val circles = points.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("pcr11jun2520h2000ml40ss-with-extracted-spots.png"))
g2.dispose()
{code}
!pcr11jun2520h2000ml40ss-with-extracted-spots.png!

h1. Under the Hood

In order to extract the regions that represent the spots we threshold at multiple levels using 2 different image treatments. The 2 image treatments are:
# Raw (no treatment)
# Standard deviation of image using a local 3x3 kernel.

We calculate a base threshold for each treatment using _maximum entropy_. Then we make multiple passes across the image from using the following:
{code}
val bound = 25 // Add and subtract this from threshold to get range
val minVal = if (split - bound < 0) split else split - bound
val maxVal = if (split + bound > 255) split else split + bound
for (i <-  minVal to maxVal by 5) {
    // Process image. ie. apply threshold and floodfill
}
{code}

For each pass across an image, we aggregate all the regions into a collection. During the aggregations we eliminate spurious or duplicate regions by:
# Exclude non-round regions. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest (e.g. {{filter(_.eccentricity()._1 < 3)}})
# Exclude regions that contain less than 10 pixels. 
# Exclude regions whose centroid duplicates an existing accepted region. (i.e. {{c1.x == c2.x && c1.y == c2.y}})
# Drop regions whose centroid is within 3 pixels of another region. These are likely to be regions that represent the same spot.


[Extracting Image Point Features 2]]]></property>
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<id name="id">19071692</id>
<property name="body"><![CDATA[h2. Extracting _Spots_ from ESP Images

h1. The BIG Picture
The first step is to read the raw tiff image:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-spots.png!

h1. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h2. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h2. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn

// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutoContrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(acImage)).filter(_.eccentricity()._1 < 3)
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-ac-spots.png!

h2. Third Pass: Dynamic Contrast (Fuzzy-Sets)
{code}
import org.mbari.esp.ia.imglib.FuzzyContrastFn
val fuzzyContrastFn = To16BitGrayFn andThen FuzzyContrastFn
val fcImage = fuzzyContrastFn(rawImage)
val fcRegions = SpotRegionsFn(rawImage, rawFloodFill(fcImage)).filter(_.eccentricity()._1 < 3)
val fcPoints = fcRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(fcImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = fcPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-fc-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-fc-spots.png!

[Extracting Image Point Features 2]]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071694</id>
<property name="body"><![CDATA[h2. Extracting _Spots_ from ESP Images

h1. The BIG Picture
The first step is to read the raw tiff image:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = imageIOService.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}
!Extracting Image Fiducial Features^pcr11jun2520h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-spots.png!

h1. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h2. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h2. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn

// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutoContrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(acImage)).filter(_.eccentricity()._1 < 3)
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-ac-spots.png!

h2. Third Pass: Dynamic Contrast (Fuzzy-Sets)
{code}
import org.mbari.esp.ia.imglib.FuzzyContrastFn
val fuzzyContrastFn = To16BitGrayFn andThen FuzzyContrastFn
val fcImage = fuzzyContrastFn(rawImage)
val fcRegions = SpotRegionsFn(rawImage, rawFloodFill(fcImage)).filter(_.eccentricity()._1 < 3)
val fcPoints = fcRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(fcImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = fcPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-fc-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-fc-spots.png!

[Extracting Image Point Features 2]]]></property>
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<property name="body"><![CDATA[]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071696</id>
<property name="body"><![CDATA[h2. Extracting _Spots_ from ESP Images

h1. The Short Version
The first step is to read the raw tiff image:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = imageIOService.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}
!Extracting Image Fiducial Features^pcr11jun2520h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.MultiPassRegionsExtractorFn
val regions = MultiPassRegionsExtractorFn(image)
val points = spotRegions.map(_.centroid).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-spots.png!

h1. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h2. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h2. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn

// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutoContrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(acImage)).filter(_.eccentricity()._1 < 3)
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-ac-spots.png!

h2. Third Pass: Dynamic Contrast (Fuzzy-Sets)
{code}
import org.mbari.esp.ia.imglib.FuzzyContrastFn
val fuzzyContrastFn = To16BitGrayFn andThen FuzzyContrastFn
val fcImage = fuzzyContrastFn(rawImage)
val fcRegions = SpotRegionsFn(rawImage, rawFloodFill(fcImage)).filter(_.eccentricity()._1 < 3)
val fcPoints = fcRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(fcImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = fcPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-fc-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-fc-spots.png!

[Extracting Image Point Features 2]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038935</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">2195697</id>
<property name="body"><![CDATA[[fluidics diagram]
# \[Fluidics tubing diagram\]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">2162932</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071697</id>
<property name="body"><![CDATA[h2. Extracting _Spots_ from ESP Images

h1. The Short Version
The first step is to read the raw tiff image:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = imageIOService.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}
!Extracting Image Fiducial Features^pcr11jun2520h2000ml40s.png!

There is a small function call that extracts the image spots. 
{code}
import org.mbari.esp.ia.imglib.MultiPassRegionsExtractorFn
val regions = MultiPassRegionsExtractorFn(image)
val points = spotRegions.map(_.centroid).toSeq
{code}
The above code snippet does the following:
# Extracts the bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{spotRegions.map(_.centroid).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of points is then converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val circles = points.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("pcr11jun2520h2000ml40ss-with-extracted-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-spots.png!

h1. Under the Hood


# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h2. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h2. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn

// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutoContrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(acImage)).filter(_.eccentricity()._1 < 3)
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-ac-spots.png!

h2. Third Pass: Dynamic Contrast (Fuzzy-Sets)
{code}
import org.mbari.esp.ia.imglib.FuzzyContrastFn
val fuzzyContrastFn = To16BitGrayFn andThen FuzzyContrastFn
val fcImage = fuzzyContrastFn(rawImage)
val fcRegions = SpotRegionsFn(rawImage, rawFloodFill(fcImage)).filter(_.eccentricity()._1 < 3)
val fcPoints = fcRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(fcImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = fcPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-fc-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-fc-spots.png!

[Extracting Image Point Features 2]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038936</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">2195698</id>
<property name="body"><![CDATA[# [Fluidics Tubing Diagram|http://http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram11-19-07.ppt]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">2162933</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071698</id>
<property name="body"><![CDATA[h2. Extracting _Spots_ from ESP Images

h1. The Short Version
The first step is to read the raw tiff image:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = imageIOService.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}
!Extracting Image Fiducial Features^pcr11jun2520h2000ml40s.png!

There is a small function call that extracts the image spots. 
{code}
import org.mbari.esp.ia.imglib.MultiPassRegionsExtractorFn
val regions = MultiPassRegionsExtractorFn(image)
val points = regions.map(_.centroid).toSeq
{code}
The above code snippet does the following:
# Extracts the bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{regions.map(_.centroid).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of points is then converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val circles = points.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("pcr11jun2520h2000ml40ss-with-extracted-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-spots.png!

h1. Under the Hood


# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h2. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h2. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn

// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutoContrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(acImage)).filter(_.eccentricity()._1 < 3)
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-ac-spots.png!

h2. Third Pass: Dynamic Contrast (Fuzzy-Sets)
{code}
import org.mbari.esp.ia.imglib.FuzzyContrastFn
val fuzzyContrastFn = To16BitGrayFn andThen FuzzyContrastFn
val fcImage = fuzzyContrastFn(rawImage)
val fcRegions = SpotRegionsFn(rawImage, rawFloodFill(fcImage)).filter(_.eccentricity()._1 < 3)
val fcPoints = fcRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(fcImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = fcPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-fc-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-fc-spots.png!

[Extracting Image Point Features 2]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038937</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">2195683</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]

h3. Engineering

# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
h4. Software Issues
# [JIRA Bug Tracker|http://mww.mbari.org/jira]

h3. Science]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071683</id>
<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment. The basic algorithm works as follows:

h1. The Alignment Algorithm

h2. The Basics

The basic building block of algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

The goal of our feature alignment is to find 


The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [linear transform|https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala] needed to rotate, scale, and align the GAL to the image and apply this to all the points in the GAL file.
# Calculate a fitness for the match between the image and GAL points. This fitness is actually a mutlipart evalucation
## First check that all the transformed GAL points are within the bounds of the image. If they are not we evaluate this match as _unfit_.
## Second, we check that the GAL points have not collapsed by calculating the most common distance between nearest neighbors. Then we check to see that this distance less than the maximum distance between image point pairs and greater then the minimum distance between point pairs.
## Finally, we use a weighted distance function. This calculates 
### the distance between all image points and all gal points. 
### Selects the GAL point nearest each image point.
### Takes the _distance_ parameter (we're using 7 pixels) and if the GAL-Image point distance is less than our distance param, we use the following {noformat}f  = fitness
d  = maximum distance [provided by user]
n  = number of image points
dn = distance from image point to nearest GAL point{noformat}
!fitnessfn.gif!]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038921</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">2195684</id>
<property name="body"><![CDATA[Meeting minutes stored in the projectlibrary:&nbsp;
# [Meeting Notes from June 7, 2007|http://oceana.shore.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc]
\\

Meeting minutes stored within Confluence:
# [08nov2007]
# [15Nov2007]]]></property>
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<id name="id">19071684</id>
<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. The basic algorithm works as follows:

h1. The Alignment Algorithm

h2. The Basics

The basic building block of algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

Why use a chromosome to represent the points? Originally, feature alignement was done using a genetic algorithm, but it's been refined so that we now use some considerable less complex. 

The goal of our feature alignment is to find a non-rigid transform that rotates, scales and translates the gal points in euclidean space to align with point features extracted from the image. The recipe for this has several steps:
# Read the GAL file and extract points for a single filter
# Extract the fiducial points from the gal points.
# Read an ESP image and extract the bright fiducial spots
# Read an ESP iamge and extract all spot features.
# Run through all the possible permutations of aligning the gal points to the image fiducial points
## Calculate the fitness for each permutation
## Select the _fittest_ alignment.



The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [linear transform|https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala] needed to rotate, scale, and align the GAL to the image and apply this to all the points in the GAL file.
# Calculate a fitness for the match between the image and GAL points. This fitness is actually a mutlipart evalucation
## First check that all the transformed GAL points are within the bounds of the image. If they are not we evaluate this match as _unfit_.
## Second, we check that the GAL points have not collapsed by calculating the most common distance between nearest neighbors. Then we check to see that this distance less than the maximum distance between image point pairs and greater then the minimum distance between point pairs.
## Finally, we use a weighted distance function. This calculates 
### the distance between all image points and all gal points. 
### Selects the GAL point nearest each image point.
### Takes the _distance_ parameter (we're using 7 pixels) and if the GAL-Image point distance is less than our distance param, we use the following {noformat}f  = fitness
d  = maximum distance [provided by user]
n  = number of image points
dn = distance from image point to nearest GAL point{noformat}
!fitnessfn.gif!]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071685</id>
<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. The basic algorithm works as follows:

h1. The Alignment Algorithm

h2. The Basics

The basic building block of algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

Why use a chromosome to represent the points? Originally, feature alignement was done using a genetic algorithm, but it's been refined so that we now use some considerable less complex. 

The goal of our feature alignment is to find a non-rigid transform that rotates, scales and translates the gal points in euclidean space to align with point features extracted from the image. The recipe for this has several steps:
# Read the GAL file and extract points for a single filter
# Extract the fiducial points from the single fitler's gal points.
# Read an ESP image and extract the bright fiducial spots
# Read an ESP iamge and extract all spot features.
# Run through all the possible permutations of aligning the gal points to the image fiducial points
## Calculate the fitness for each permutation
## Select the _fittest_ alignment.



The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [linear transform|https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala] needed to rotate, scale, and align the GAL to the image and apply this to all the points in the GAL file.
# Calculate a fitness for the match between the image and GAL points. This fitness is actually a mutlipart evalucation
## First check that all the transformed GAL points are within the bounds of the image. If they are not we evaluate this match as _unfit_.
## Second, we check that the GAL points have not collapsed by calculating the most common distance between nearest neighbors. Then we check to see that this distance less than the maximum distance between image point pairs and greater then the minimum distance between point pairs.
## Finally, we use a weighted distance function. This calculates 
### the distance between all image points and all gal points. 
### Selects the GAL point nearest each image point.
### Takes the _distance_ parameter (we're using 7 pixels) and if the GAL-Image point distance is less than our distance param, we use the following {noformat}f  = fitness
d  = maximum distance [provided by user]
n  = number of image points
dn = distance from image point to nearest GAL point{noformat}
!fitnessfn.gif!]]></property>
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</property>
</object>
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<property name="body"><![CDATA[h2. Quotes
# Sphere casting [(Wah Change)][http://]]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071686</id>
<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. The basic algorithm works as follows:

h1. The Alignment Algorithm

h2. The Basics

The basic building block of algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

Why use a chromosome to represent the points? Originally, feature alignement was done using a genetic algorithm, but it's been refined so that we now use some considerable less complex. 

The goal of our feature alignment is to find a non-rigid transform that rotates, scales and translates the gal points in euclidean space to align with point features extracted from the image. The recipe for this has several steps:
# [Read the GAL file and extract points for a single filter|Extracting GAL Point Features]
# Extract the fiducial points from the single fitler's gal points.
# Read an ESP image and extract the bright fiducial spots
# Read an ESP iamge and extract all spot features.
# Run through all the possible permutations of aligning the gal points to the image fiducial points
## Calculate the fitness for each permutation
## Select the _fittest_ alignment.



The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [linear transform|https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala] needed to rotate, scale, and align the GAL to the image and apply this to all the points in the GAL file.
# Calculate a fitness for the match between the image and GAL points. This fitness is actually a mutlipart evalucation
## First check that all the transformed GAL points are within the bounds of the image. If they are not we evaluate this match as _unfit_.
## Second, we check that the GAL points have not collapsed by calculating the most common distance between nearest neighbors. Then we check to see that this distance less than the maximum distance between image point pairs and greater then the minimum distance between point pairs.
## Finally, we use a weighted distance function. This calculates 
### the distance between all image points and all gal points. 
### Selects the GAL point nearest each image point.
### Takes the _distance_ parameter (we're using 7 pixels) and if the GAL-Image point distance is less than our distance param, we use the following {noformat}f  = fitness
d  = maximum distance [provided by user]
n  = number of image points
dn = distance from image point to nearest GAL point{noformat}
!fitnessfn.gif!]]></property>
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</property>
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<property name="body"><![CDATA[h2. Quotes

# Sphere casting [(Wah Change)]]]></property>
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</property>
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<id name="id">19071687</id>
<property name="body"><![CDATA[h2. Extracting _Spots_ from ESP Images

h1. The BIG Picture
The first step is to read the raw tiff image:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-spots.png!

h1. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h2. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h2. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn

// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutoContrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(acImage)).filter(_.eccentricity()._1 < 3)
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-ac-spots.png!

h2. Third Pass: Dynamic Contrast (Fuzzy-Sets)
{code}
import org.mbari.esp.ia.imglib.FuzzyContrastFn
val fuzzyContrastFn = To16BitGrayFn andThen FuzzyContrastFn
val fcImage = fuzzyContrastFn(rawImage)
val fcRegions = SpotRegionsFn(rawImage, rawFloodFill(fcImage)).filter(_.eccentricity()._1 < 3)
val fcPoints = fcRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(fcImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = fcPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-fc-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-fc-spots.png!]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">2195688</id>
<property name="body"><![CDATA[h2. Quotes

# Sphere casting [(Wah Chang)|^Wah Chang quote MBARI 60200 11-14 C5.pdf]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">2162922</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">2195689</id>
<property name="body"><![CDATA[h2. Quotes

* Sphere casting [(Wah Chang)|^Wah Chang quote MBARI 60200 11-14 C5.pdf]
* Machining
** [Tapemation|^Wah Chang quote MBARI 60200 11-14 C5.pdf]
** Hanard Machine]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">2195690</id>
<property name="body"><![CDATA[h2. Quotes

* Sphere casting [(Wah Chang)|^Wah Chang quote MBARI 60200 11-14 C5.pdf]
* Machining
** [Tapemation|^Wah Chang quote MBARI 60200 11-14 C5.pdf]
** Hanard Machine (sent for quote 11-15-07)]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">2162924</id>
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</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071690</id>
<property name="body"><![CDATA[h2. Extracting _Spots_ from ESP Images

h1. The BIG Picture
The first step is to read the raw tiff image:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-spots.png!

h1. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h2. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h2. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn

// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutoContrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(acImage)).filter(_.eccentricity()._1 < 3)
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-ac-spots.png!

h2. Third Pass: Dynamic Contrast (Fuzzy-Sets)
{code}
import org.mbari.esp.ia.imglib.FuzzyContrastFn
val fuzzyContrastFn = To16BitGrayFn andThen FuzzyContrastFn
val fcImage = fuzzyContrastFn(rawImage)
val fcRegions = SpotRegionsFn(rawImage, rawFloodFill(fcImage)).filter(_.eccentricity()._1 < 3)
val fcPoints = fcRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(fcImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = fcPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-fc-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-fc-spots.png!]]></property>
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</property>
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<id name="id">19071681</id>
<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment. The basic algorithm works as follows:

h2. The Alignment Algorithm

The basic building block of algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [linear transform|https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala] needed to rotate, scale, and align the GAL to the image and apply this to all the points in the GAL file.
# Calculate a fitness for the match between the image and GAL points. This fitness is actually a mutlipart evalucation
## First check that all the transformed GAL points are within the bounds of the image. If they are not we evaluate this match as _unfit_.
## Second, we check that the GAL points have not collapsed by calculating the most common distance between nearest neighbors. Then we check to see that this distance less than the maximum distance between image point pairs and greater then the minimum distance between point pairs.
## Finally, we use a weighted distance function. This calculates 
### the distance between all image points and all gal points. 
### Selects the GAL point nearest each image point.
### Takes the _distance_ parameter (we're using 7 pixels) and if the GAL-Image point distance is less than our distance param, we use the following {noformat}f  = fitness
d  = maximum distance [provided by user]
n  = number of image points
dn = distance from image point to nearest GAL point{noformat}
!fitnessfn.gif!]]></property>
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<id name="id">19071678</id>
<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment. The basic algorithm works as follows:

h2. The Genetic Algorithm

The basic building block of our genetic algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [linear transform|https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala] needed to rotate, scale, and align the GAL to the image and apply this to all the points in the GAL file.
# Calculate a fitness for the match between the image and GAL points. This fitness is actually a mutlipart evalucation
## First check that all the transformed GAL points are within the bounds of the image. If they are not we evaluate this match as _unfit_.
## Second, we check that the GAL points have not collapsed by calculating the most common distance between nearest neighbors. Then we check to see that this distance less than the maximum distance between image point pairs and greater then the minimum distance between point pairs.
## Finally, we use a weighted distance function. This calculates 
### the distance between all image points and all gal points. 
### Selects the GAL point nearest each image point.
### Takes the _distance_ parameter (we're using 7 pixels) and if the GAL-Image point distance is less than our distance param, we use the following {noformat}f  = fitness
d  = maximum distance [provided by user]
n  = number of image points
dn = distance from image point to nearest GAL point{noformat}
!fitnessfn.gif!]]></property>
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<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = imageIOService.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}

!pcr11jun2520h2000ml40s.png!

h2. Extracting Bright Spots

The fiducials are typically the brightest areas on the image, especially in contrast to pixels immediately adjacent to the fiducial spots. We take advantage of this quality and isolate the fiducials by calculating the standard deviation of a 3x3 kernel across the entire image. The reason is clearly evident when looking at a surface plot of the raw image vs. the standard deviation. On the raw image, the fiducials may not be distinct from noisy backgrounds. However, when when using the standard deviation the fiducials sharply contrast with the rest of the image. In the images below, the 3 brightest peaks are the fiducial spots on the image.

!rawimage.png|width=900!
!stdimage.png|width=900!

We can extract the bright regions with the following code:
{code}
import org.mbari.esp.ia.imglib.BrightSpotExtractorFn
val regions = BrightSpotExtractorFn(rawImage)
{code}

{info:title:BrightSpotExtractorFn}
The internals of this function use a very standard pattern for spot extraction. The steps boil down to:
# Convert the image to 8-bit Gray so that we can calculate the histogram very quickly.
# Threshold the image using _maximum entropy_. _Renyi's entropy_ also works well but takes longer to calculate.
# Convert the binary threhold image to 16-bit *before* flood filling. Sometimes there is more than 256 regions, which can not be represented in an 8-bit image.
# Remove the area outside of a central circle. In general, we use a circle radius of 75% of the minimum radius of an image.
# Flood fill

Here's the function in it's entirety:
{code}
package org.mbari.esp.ia.imglib

import ij.process.ImageProcessor
import org.mbari.esp.ia.awt.ShortRegion

object BrightSpotExtractorFn extends (ImageProcessor => Iterable[ShortRegion]) {

    def apply(from: ImageProcessor): Iterable[ShortRegion] = {
        // Calculate local standard deviation for every 3x3 block of pixels
        val to = StdFn(from)

        val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
        val floodFill = {
            val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
            val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
            To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
        }
        val fill = threshold andThen floodFill

        SpotRegionsFn(from, fill(to))

    }
}

{code}
{info}

Then draw the image as follows:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val points = regions.map(_.centroid)
val circles = points.map(p => new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))

val colorImage = ToRGBFn(image).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
io.write(colorImage, new File("pcr11jun2520h2000ml40s-with-extracted-fiducials.png"))
g2.dispose()
{code}

!pcr11jun2520h2000ml40s-with-extracted-fiducials.png!]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071665</id>
<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = imageIOService.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}

!pcr11jun2520h2000ml40s.png!

h2. Extracting Bright Spots

The fiducials are typically the brightest areas on the image, especially in contrast to pixels immediately adjacent to the fiducial spots. We take advantage of this quality and isolate the fiducials by calculating the standard deviation of a 3x3 kernel across the entire image. The reason is clearly evident when looking at a surface plot of the raw image vs. the standard deviation. On the raw image, the fiducials may not be distinct from noisy backgrounds. However, when when using the standard deviation the fiducials sharply contrast with the rest of the image. In the images below, the 3 brightest peaks are the fiducial spots on the image.

!rawimage.png|width=900!
!stdimage.png|width=900!

We can extract the bright regions with the following code:
{code}
import org.mbari.esp.ia.imglib.BrightSpotExtractorFn
val regions = BrightSpotExtractorFn(rawImage)
{code}

{info:title:BrightSpotExtractorFn}
The internals of this function use a very standard pattern for spot extraction. Here's the function in it's entirety:
{code}
package org.mbari.esp.ia.imglib

import ij.process.ImageProcessor
import org.mbari.esp.ia.awt.ShortRegion

object BrightSpotExtractorFn extends (ImageProcessor => Iterable[ShortRegion]) {

    def apply(from: ImageProcessor): Iterable[ShortRegion] = {
        // Calculate local standard deviation for every 3x3 block of pixels
        val to = StdFn(from)

        val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
        val floodFill = {
            val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
            val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
            To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
        }
        val fill = threshold andThen floodFill

        SpotRegionsFn(from, fill(to))

    }
}

{code}
{info}

Then draw the image as follows:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val points = regions.map(_.centroid)
val circles = points.map(p => new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))

val colorImage = ToRGBFn(image).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
io.write(colorImage, new File("pcr11jun2520h2000ml40s-with-extracted-fiducials.png"))
g2.dispose()
{code}

!pcr11jun2520h2000ml40s-with-extracted-fiducials.png!]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071659</id>
<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = imageIOService.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}

!pcr11jun2520h2000ml40s.png!

h2. Extracting Bright Spots

The fiducials are typically the brightest areas on the image, especially in contrast to pixels immediately adjacent to the fiducial spots. We take advantage of this quality and isolate the fiducials by calculating the standard deviation of a 3x3 kernel across the entire image. The reason is clearly evident when looking at a surface plot of the raw image vs. the standard deviation. On the raw image, the fiducials may not be distinct from noisy backgrounds. However, when when using the standard deviation the fiducials sharply contrast with the rest of the image. In the images below, the 3 brightest peaks are the fiducial spots on the image.

!rawimage.png|width=900!
!stdimage.png|width=900!

We can extract the bright regions with the following code:
{code}
import org.mbari.esp.ia.imglib.BrightSpotExtractorFn
val regions = BrightSpotExtractorFn(rawImage)
{code}

{info:title:BrightSpotExtractorFn}
The internals of this function use a very standard pattern for spot extraction. Here's the function in it's entirety:
{code}
package org.mbari.esp.ia.imglib

import ij.process.ImageProcessor
import org.mbari.esp.ia.awt.ShortRegion

object BrightSpotExtractorFn extends (ImageProcessor => Iterable[ShortRegion]) {

    def apply(from: ImageProcessor): Iterable[ShortRegion] = {
        // Calculate local standard deviation for every 3x3 block of pixels
        val to = StdFn(from)

        val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
        val floodFill = {
            val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
            val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
            To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
        }
        val fill = threshold andThen floodFill

        SpotRegionsFn(from, fill(to))

    }
}

{code}

{note}

Then draw the image as follows:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val points = regions.map(_.centroid)
val circles = points.map(p => new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))

val colorImage = ToRGBFn(image).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
io.write(colorImage, new File("pcr11jun2520h2000ml40s-with-extracted-fiducials.png"))
g2.dispose()
{code}

!pcr11jun2520h2000ml40s-with-extracted-fiducials.png!]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071657</id>
<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = imageIOService.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}

!pcr11jun2520h2000ml40s.png!

h2. Extracting Bright Spots

The fiducials are typically the brightest areas on the image, especially in contrast to pixels immediately adjacent to the fiducial spots. We take advantage of this quality and isolate the fiducials by calculating the standard deviation of a 3x3 kernel across the entire image. The reason is clearly evident when looking at a surface plot of the raw image vs. the standard deviation. On the raw image, the fiducials may not be distinct from noisy backgrounds. However, when when using the standard deviation the fiducials sharply contrast with the rest of the image. In the images below, the 3 brightest peaks are the fiducial spots on the image.

!rawimage.png|width=900!
!stdimage.png|width=900!

We can extract the bright regions with the following code:
{code}
import org.mbari.esp.ia.imglib.BrightSpotExtractorFn
val regions = BrightSpotExtractorFn(rawImage)
{code}

{note:title:BrightSpotExtractorFn}
The internals of this function use a very standard pattern for spot extraction. Here's the function in it's entirety:
{code}
package org.mbari.esp.ia.imglib

import ij.process.ImageProcessor
import org.mbari.esp.ia.awt.ShortRegion

object BrightSpotExtractorFn extends (ImageProcessor => Iterable[ShortRegion]) {

    def apply(from: ImageProcessor): Iterable[ShortRegion] = {
        // Calculate local standard deviation for every 3x3 block of pixels
        val to = StdFn(from)

        val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
        val floodFill = {
            val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
            val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
            To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
        }
        val fill = threshold andThen floodFill

        SpotRegionsFn(from, fill(to))

    }
}

{code}

{note}

Then draw the image as follows:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val points = regions.map(_.centroid)
val circles = points.map(p => new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))

val colorImage = ToRGBFn(image).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
io.write(colorImage, new File("pcr11jun2520h2000ml40s-with-extracted-fiducials.png"))
g2.dispose()
{code}

!pcr11jun2520h2000ml40s-with-extracted-fiducials.png!]]></property>
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</property>
</object>
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<id name="id">2195594</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!

# [GUI Component Development Pages|2G ESP GUI Project Page]]]></property>
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</property>
</object>
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<id name="id">2195592</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!

# GUI Component Development Pages]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071656</id>
<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = imageIOService.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}

!pcr11jun2520h2000ml40s.png!

h2. Extracting Bright Spots

The fiducials are typically the brightest areas on the image, especially in contrast to pixels immediately adjacent to the fiducial spots. We take advantage of this quality and isolate the fiducials by calculating the standard deviation of a 3x3 kernel across the entire image. The reason is clearly evident when looking at a surface plot of the raw image vs. the standard deviation. On the raw image, the fiducials may not be distinct from noisy backgrounds. However, when when using the standard deviation the fiducials sharply contrast with the rest of the image. In the images below, the 3 brightest peaks are the fiducial spots on the image.

!rawimage.png|width=900!
!stdimage.png|width=900!

We can extract the bright regions with the following code:
{code}
import org.mbari.esp.ia.imglib.BrightSpotExtractorFn
val regions = BrightSpotExtractorFn(rawImage)
{code}

Then draw the image as follows:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val points = regions.map(_.centroid)
val circles = points.map(p => new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))

val colorImage = ToRGBFn(image).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
io.write(colorImage, new File("pcr11jun2520h2000ml40s-with-extracted-fiducials.png"))
g2.dispose()
{code}

!pcr11jun2520h2000ml40s-with-extracted-fiducials.png!]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038894</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071653</id>
<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val io = ToolBox.imageIOService
val image = imageIOService.read(new URL("file:/test08/pcr11jun2520h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
io.write(image, new File("pcr11jun2520h2000ml40s.png"))
{code}

!pcr11jun2520h2000ml40s.png!

h2. Extracting Bright Spots

The fiducials are typically the brightest areas on the image, especially in contrast to pixels immediately adjacent to the fiducial spots. We take advantage of this quality and isolate the fiducials by calculating the standard deviation of a 3x3 kernel across the entire image. The reason is clearly evident when looking at a surface plot of the raw image vs. the standard deviation. On the raw image, the fiducials may not be distinct from noisy backgrounds. However, when when using the standard deviation the fiducials sharply contrast with the rest of the image. In the images below, the 3 brightest peaks are the fiducial spots on the image.

!rawimage.png|width=900!
!stdimage.png|width=900!

We can extract the bright regions with the following code:
{code}
import org.mbari.esp.ia.imglib.BrightSpotExtractorFn
val regions = BrightSpotExtractorFn(rawImage)
{code}

Then draw the image as follows:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val points = regions.map(_.centroid)
val circles = points.map(p => new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))

val colorImage = ToRGBFn(image).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
io.write(colorImage, new File("pcr11jun2520h2000ml40s-with-extracted-fiducials.png"))
g2.dispose()
{code}]]></property>
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</property>
</object>
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<id name="id">2195590</id>
<property name="body"><![CDATA[Welcome to the ESP -- SURF Center project!

# GUI Component Development Pages]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">2162823</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071652</id>
<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test08/pcr11jun0700h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("pcr11jun0700h2000ml40s.png"))
{code}

!pcr11jun2520h2000ml40s.png!

h2. Extracting Bright Spots

The fiducials are typically the brightest areas on the image, especially in contrast to pixels immediately adjacent to the fiducial spots. We take advantage of this quality and isolate the fiducials by calculating the standard deviation of a 3x3 kernel across the entire image. The reason is clearly evident when looking at a surface plot of the raw image vs. the standard deviation. On the raw image, the fiducials may not be distinct from noisy backgrounds. However, when when using the standard deviation the fiducials sharply contrast with the rest of the image. In the images below, the 3 brightest peaks are the fiducial spots on the image.

!rawimage.png|width=900!
!stdimage.png|width=900!

We can extract the bright regions with the following code:
{code}
import org.mbari.esp.ia.imglib.BrightSpotExtractorFn
val regions = BrightSpotExtractorFn(rawImage)
{code}

Then draw the image as follows:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val points = regions.map(_.centroid)
val circles = points.map(p => new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
g2.setPaint(Color.GREEN)
circles.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("pcr11jun0700h2000ml40s-with-extracted-fiducials.png"))
g2.dispose()
{code}]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071648</id>
<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test08/pcr11jun0700h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}

!pcr11jun2520h2000ml40s.png!

h2. Extracting Bright Spots

The fiducials are typically the brightest areas on the image, especially in contrast to pixels immediately adjacent to the fiducial spots. We take advantage of this quality and isolate the fiducials by calculating the standard deviation of a 3x3 kernel across the entire image. The reason is clearly evident when looking at a surface plot of the raw image vs. the standard deviation. On the raw image, the fiducials may not be distinct from noisy backgrounds. However, when when using the standard deviation the fiducials sharply contrast with the rest of the image. In the images below, the 3 brightest peaks are the fiducial spots on the image.

!rawimage.png|width=900!
!stdimage.png!]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038886</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071647</id>
<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test08/pcr11jun0700h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}

!pcr11jun2520h2000ml40s.png!

h2. Extracting Bright Spots

The fiducials are typically the brightest areas on the image, especially in contrast to pixels immediately adjacent to the fiducial spots. We take advantage of this quality and isolate the fiducials by calculating the standard deviation of a 3x3 kernel across the entire image. The reason is clearly evident when looking at a surface plot of the raw image vs. the standard deviation. On the raw image, the fiducials may not be distinct from noisy backgrounds. However, when when using the standard deviation the fiducials sharply contrast with the rest of the image. In the images below, the 3 brightest peaks are the fiducial spots on the image.

!rawimage.png|width=400!
!stdimage.png!]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038885</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071650</id>
<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test08/pcr11jun0700h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}

!pcr11jun2520h2000ml40s.png!

h2. Extracting Bright Spots

The fiducials are typically the brightest areas on the image, especially in contrast to pixels immediately adjacent to the fiducial spots. We take advantage of this quality and isolate the fiducials by calculating the standard deviation of a 3x3 kernel across the entire image. The reason is clearly evident when looking at a surface plot of the raw image vs. the standard deviation. On the raw image, the fiducials may not be distinct from noisy backgrounds. However, when when using the standard deviation the fiducials sharply contrast with the rest of the image. In the images below, the 3 brightest peaks are the fiducial spots on the image.

!rawimage.png|width=900!
!stdimage.png|width=900!]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038888</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">2195644</id>
<property name="body"><![CDATA[Meeting minutes stored in the projectlibrary:&nbsp;

# [Meeting Notes from June 7, 2007|http://oceana.shore.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc]
# [November 7, 2007]]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071644</id>
<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test08/pcr11jun0700h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}

!pcr11jun2520h2000ml40s.png!

h2. Extracting Bright Spots

The fiducials are typically the brightest areas on the image, especially in contrast to pixels immediately adjacent to the fiducial spots. We take advantage of this quality and isolate the fiducials by calculating the standard deviation of a 3x3 kernel across the entire image.]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">2195643</id>
<property name="body"><![CDATA[Meeting minutes stored in the projectlibrary:&nbsp;

#[Meeting Notes from June 7, 2007|http://oceana.shore.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc]
#[November 7, 2007]]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071646</id>
<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test08/pcr11jun0700h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}

!pcr11jun2520h2000ml40s.png!

h2. Extracting Bright Spots

The fiducials are typically the brightest areas on the image, especially in contrast to pixels immediately adjacent to the fiducial spots. We take advantage of this quality and isolate the fiducials by calculating the standard deviation of a 3x3 kernel across the entire image. The reason is clearly evident when looking at a surface plot of the raw image vs. the standard deviation. On the raw image, the fiducials may not be distinct from noisy backgrounds. However, when when using the standard deviation the fiducials sharply contrast with the rest of the image. In the images below, the 3 brightest peaks are the fiducial spots on the image.

!rawimage.png!
!stdimage.png!]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">21004722</id>
<property name="body"><![CDATA[Instrument Level
|| || Control Loops&nbsp; || || Inputs \\ || Outputs || || || || || ||
| 1 \\ | Sampling Pump \\ | | | | | | | | |
| 2 | Spool Valve Selector \\ | | | | | | | | |
| 3 | Cylinder Rotate \\ | | | | | | | | |
| 4 | Cartridge Actuator Alignment \\ | | | | | | | | |
| 5 | Cartridge Actuator 1 \\ | | | | | | | | |
| 6 | Cartridge Actuator 2 | | | | | | | | |
| 7 | Cartridge Actuator 3 | | | | | | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | | | | | | |
| 9 | Cartridge Reagent Valve \\ | | | | | | | | |
| 10 | A/M Clamp \\ | | | | | | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | | | | | | |
| 12 | A/M Hand-off Syringe \\ | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |

|| || Discrete Actions || || \\ || Outputs || || || || || ||
| 1 \\ | Intake Select 1 \\ | | | | | | | | |
| 2 | Intake Select 2 \\ | | | | | | | | |
| 3 | Bulkhead valve (intake) \\ | | | | | | | | |
| 4 | Bulkhead valve (exhaust) | | | | | | | | |
| 5 | Cartridge Valve Actuator 1 \\ | | | | | | | | |
| 6 | Cylinder latch \\ | | | | | | | | |
| 7 | A/M Valve 1 \\ | | | | | | | | |
| 8 | A/M Valve 2 \\ | | | | | | | | |
| 9 | A/M Valve 3 | | | | | | | | |
| 10 | A/M Valve 4 | | | | | | | | |
| 11 | A/M Clamp \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |
\\

Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
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<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test08/pcr11jun0700h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}

!pcr11jun2520h2000ml40s.png!

h2. Extracting Bright Spots

The fiducials are typically the brightest areas on the image, especially in contrast to pixels immediately adjacent to the fiducial spots. We take advantage of this quality and isolate the fiducials by calculating the standard deviation of a 3x3 kernel across the entire image. The reason is clearly evident when looking at a surface plot of the raw image vs. the standard deviation. On the raw image, the fiducials may not be distinct from noisy backgrounds. However, when when using the standard deviation the fiducials sharply contrast with the rest of the image.

!rawimage.png!
!stdimage.png!]]></property>
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<property name="body"><![CDATA[Meeting minutes stored in the projectlibrary:&nbsp;

[http://oceana.shore.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc]]]></property>
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<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test08/pcr11jun0700h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}]]></property>
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<property name="body"><![CDATA[Meeting minutes stored in the projectlibrary:&nbsp;

[file:///Volumes/projectlibrary/ESP/ESP.meetings.minutes/]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">2162873</id>
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<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}
]]></property>
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<property name="body"><![CDATA[Meeting minutes stored in the projectlibrary:&nbsp;

[Meeting Notes from June 7, 2007|http://oceana.shore.mbari.org/ProjectLibrary/ESP/ESP.meetings.minutes/ESP%20Planning%20Mtng%2007Jun07.doc]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">2162876</id>
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<property name="body"><![CDATA[h2. Extracting the Fiducial Spots from Images

{note:title=Assumptions}
The technique used here assumes that the fiducial spots on the image are *very* bright compared to the rest of the image
{note}

h1. Reading the Image

{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test08/pcr11jun0700h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}

!pcr11jun2520h2000ml40s.png!]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!

# [GUI Component Development Pages|2G ESP GUI Project Page]
# Micro-Fluidics Block]]></property>
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<property name="body"><![CDATA[file:///Volumes/projectlibrary/ESP/ESP.meetings.minutes/]]></property>
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<property name="body"><![CDATA[h2. Overview of ESP Image Analysis Automation

# [Investigations into Automated Image Analysis]
# [Extracting GAL Point Features]
# [Extracting Image Point Features]
# [Point Feature Alignment]

h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!

# [GUI Component Development Pages|2G ESP GUI Project Page]
# Micro-Fluidics Block]]></property>
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<property name="body"><![CDATA[[G3 Process Diagrams|^G3process-04-12-12.pptx]Revised: April 12, 2012

[Modular Cartridge Diagrams|^G3 Modular Cartridge 04-30-12.pptx]Revised: April 30, 2012

[^G3 Modular Cartridge 05-02-12.pptx] Revised: May 2, 2012]]></property>
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<property name="body"><![CDATA[[HAB-DA Process Diagram|^G3HABDA-0.1.pptx]Ver 0.1

[HAB-DA Cartridge written protocol|^3G_HABDA_Ver0.1.doc]Ver 0.1
\\ [^G3 Modular Cartridge 05-02-12.pptx] Revised: May 2, 2012]]></property>
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<property name="body"><![CDATA[[HAB-DA Process Diagram|^G3HABDA-0.1.pptx]Ver 0.1[HAB-DA Cartridge written protocol|^3G_HABDA_Ver0.1.doc]Ver 0.1

\\  [^G3 Modular Cartridge 05-02-12.pptx] Revised: May 2, 2012]]></property>
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<property name="body"><![CDATA[
Instrument Level
|| || Control Loops&nbsp; || || Inputs \\ || Outputs || || || || || ||
| 1 \\ | Sampling Pump \\ | | | | | | | | |
| 2 | Spool Valve Selector \\ | | | | | | | | |
| 3 | Cylinder Rotate \\ | | | | | | | | |
| 4 | Cartridge Actuator Alignment \\ | | | | | | | | |
| 5 | Cartridge Actuator 1 \\ | | | | | | | | |
| 6 | Cartridge Actuator 2 | | | | | | | | |
| 7 | Cartridge Actuator 3 | | | | | | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | | | | | | |
| 9 | Cartridge Reagent Valve \\ | | | | | | | | |
| 10 | A/M Clamp \\ | | | | | | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | | | | | | |
| 12 | A/M Hand-off Syringe \\ | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |

|| || Discrete Actions || || \\ || Outputs || || || || || ||
| 1 \\ | Intake Select 1 \\ | | | | | | | | |
| 2 | Intake Select 2 \\ | | | | | | | | |
| 3 | Bulkhead valve (intake) \\ | | | | | | | | |
| 4 | Bulkhead valve (exhaust) | | | | | | | | |
| 5 | Cartridge Valve Actuator 1 \\ | | | | | | | | |
| 6 | Cylinder latch \\ | | | | | | | | |
| 7 | A/M Valve 1 \\ | | | | | | | | |
| 8 | A/M Valve 2 \\ | | | | | | | | |
| 9 | A/M Valve 3 | | | | | | | | |
| 10 | A/M Valve 4 | | | | | | | | |
| 11 | A/M Clamp \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |
\\

Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
\\]]></property>
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<property name="body"><![CDATA[{gliffy:name=Electronic layout|space=ESPAPP|page=G3 IO list - Control loops|pageid=19040250|align=left|size=L}
Instrument Level
|| || Control Loops&nbsp; || || Inputs \\ || Outputs || || || || || ||
| 1 \\ | Sampling Pump \\ | | | | | | | | |
| 2 | Spool Valve Selector \\ | | | | | | | | |
| 3 | Cylinder Rotate \\ | | | | | | | | |
| 4 | Cartridge Actuator Alignment \\ | | | | | | | | |
| 5 | Cartridge Actuator 1 \\ | | | | | | | | |
| 6 | Cartridge Actuator 2 | | | | | | | | |
| 7 | Cartridge Actuator 3 | | | | | | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | | | | | | |
| 9 | Cartridge Reagent Valve \\ | | | | | | | | |
| 10 | A/M Clamp \\ | | | | | | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | | | | | | |
| 12 | A/M Hand-off Syringe \\ | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |

|| || Discrete Actions || || \\ || Outputs || || || || || ||
| 1 \\ | Intake Select 1 \\ | | | | | | | | |
| 2 | Intake Select 2 \\ | | | | | | | | |
| 3 | Bulkhead valve (intake) \\ | | | | | | | | |
| 4 | Bulkhead valve (exhaust) | | | | | | | | |
| 5 | Cartridge Valve Actuator 1 \\ | | | | | | | | |
| 6 | Cylinder latch \\ | | | | | | | | |
| 7 | A/M Valve 1 \\ | | | | | | | | |
| 8 | A/M Valve 2 \\ | | | | | | | | |
| 9 | A/M Valve 3 | | | | | | | | |
| 10 | A/M Valve 4 | | | | | | | | |
| 11 | A/M Clamp \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |
\\

Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
\\]]></property>
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<property name="body"><![CDATA[{gliffy:name=Electrical Layout|space=ESPAPP|page=G3 IO list - Control loops|pageid=19040250|align=left|size=L}

Instrument Level
|| || Control Loops&nbsp; || || Inputs \\ || Outputs || || || || || ||
| 1 \\ | Sampling Pump \\ | | | | | | | | |
| 2 | Spool Valve Selector \\ | | | | | | | | |
| 3 | Cylinder Rotate \\ | | | | | | | | |
| 4 | Cartridge Actuator Alignment \\ | | | | | | | | |
| 5 | Cartridge Actuator 1 \\ | | | | | | | | |
| 6 | Cartridge Actuator 2 | | | | | | | | |
| 7 | Cartridge Actuator 3 | | | | | | | | |
| 8 | Cartridge Actuator Puck Evac \\ | | | | | | | | |
| 9 | Cartridge Reagent Valve \\ | | | | | | | | |
| 10 | A/M Clamp \\ | | | | | | | | |
| 11 | A/M Clamp Radial Alignment \\ | | | | | | | | |
| 12 | A/M Hand-off Syringe \\ | | | | | | | | |
| | | | | | | | | | |
| | | | | | | | | | |

|| || Discrete Actions || || \\ || Outputs || || || || || ||
| 1 \\ | Intake Select 1 \\ | | | | | | | | |
| 2 | Intake Select 2 \\ | | | | | | | | |
| 3 | Bulkhead valve (intake) \\ | | | | | | | | |
| 4 | Bulkhead valve (exhaust) | | | | | | | | |
| 5 | Cartridge Valve Actuator 1 \\ | | | | | | | | |
| 6 | Cylinder latch \\ | | | | | | | | |
| 7 | A/M Valve 1 \\ | | | | | | | | |
| 8 | A/M Valve 2 \\ | | | | | | | | |
| 9 | A/M Valve 3 | | | | | | | | |
| 10 | A/M Valve 4 | | | | | | | | |
| 11 | A/M Clamp \\ | | | | | | | | |
| 12 | \\ | | | | | | | | |
| \\ | \\ | \\ | \\ | | | | | | |
\\

Cartridge Level Control Loops
|| || Cartridge Control Loops \\ || || Inputs \\ || Outputs ||
| 1 \\ | Puck Heater (70, 85C) \\ | | | |
| 2 | Puck beating \\ | | | |
| 3 | Microsonic Actuation \\ | | | |
| 4 | Heater 2 (Ab Mixer, 30C) \\ | | | |
| 5 | Heater 3 (Filtrate module, 30C) | | | |
| 6 | Heater 4 (Filtrate Ab Mixer, 30C) | | | |
| 7 | \\ | | | |
| 8 | \\ | | | |
| 9 | \\ | | | |
| 10 | \\ | | | |
| 11 | \\ | | | |
| 12 | \\ | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:Resolving Spots Issue #1}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots.{info}
{info:Resolving Spots Issue #2} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{Info:title=Resolving Spots Issue #3}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}


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<id name="id">9830928</id>
<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:Resolving Spots Issue #1}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots.{info}
{info:Resolving Spots Issue #2} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}


{note:title=Segmentation isn't reliable}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{note}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:Resolving Spots Issue #1}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots.{info}
* Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.

{note:title=Segmentation isn't reliable}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{note}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
* *NOTE*: In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. 
* Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.

{note:title=Segmentation isn't reliable}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{note}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
* !fitler_3_aoi.png!
* {code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
* !fitler_3_aoi_masked.png!
* *NOTE*: In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. 
* Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.

{note:title=Segmentation isn't reliable}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{note}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
{code}
* *NOTE*: In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. 
* Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.

{note:title=Segmentation isn't reliable}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{note}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
# Remove areas outside the filter boundaries from the filter analysis.
#* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
#* This is important since the edge of the disk creates high intensity artifacts in the filter image.
#* !fitler_3_aoi.png!
# * {code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}
# Apply a thresholding technique to locate spots. 
#* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
#* !fitler_3_aoi_masked.png!
#* *NOTE*: In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. 
#* Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.

{note:title=Segmentation isn't reliable}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{note}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
# Remove areas outside the filter boundaries from the filter analysis.
#* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
#* This is important since the edge of the disk creates high intensity artifacts in the filter image.
#* !fitler_3_aoi.png!
# Apply a thresholding technique to locate spots. 
#* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
#* !fitler_3_aoi_masked.png!
#* *NOTE*: In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. 
#* Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.

{note:title=Segmentation isn't reliable}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{note}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3){code}




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<id name="id">9830944</id>
<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3){code}




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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
Map pointMap = gaas.extractIntensities(ip, 3){code}




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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.




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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #2: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!
{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots.{info}
{info:title=Resolving Spots Issue #2: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!
{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots.{info}
{info:title=Resolving Spots Issue #2: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!
{info)
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:Resolving Spots Issue #1}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots.{info}
{info:Resolving Spots Issue #2} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #3}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}


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<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment. The basic algorithm works as follows:

h2. The Genetic Algorithm

The basic building block of our genetic algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [linear transform|https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala] needed to rotate, scale, and align the GAL to the image and apply this to all the points in the GAL file.
# Calculate a fitness for the match between the image and GAL points. This fitness is actually a mutlipart evalucation
## First check that all the transformed GAL points are within the bounds of the image. If they are not we evaluate this match as _unfit_.
## Second, we check that the GAL points have not collapsed by calculating the most common distance between nearest neighbors. Then we check to see that this distance less than the maximum distance between image point pairs and greater then the minimum distance between point pairs.
## Finally, we use a weighted distance function. This calculates 
### the distance between all image points and all gal points. 
### Selects the GAL point nearest each image point.
### Takes the _distance_ parameter (we're using 7 pixels) and if the GAL-Image point distance is less than our distance param, we use the following {noformat}f=fitness, d = maximum distance, n = number of image points, dn = distance from image point to nearest GAL point{noformat} : 
!fitnessfn.gif!]]></property>
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<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment. The basic algorithm works as follows:

h2. The Genetic Algorithm

The basic building block of our genetic algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [linear transform|https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala] needed to rotate, scale, and align the GAL to the image and apply this to all the points in the GAL file.
# Calculate a fitness for the match between the image and GAL points. This fitness is actually a mutlipart evalucation
## First check that all the transformed GAL points are within the bounds of the image. If they are not we evaluate this match as _unfit_.
## Second, we check that the GAL points have not collapsed by calculating the most common distance between nearest neighbors. Then we check to see that this distance less than the maximum distance between image point pairs and greater then the minimum distance between point pairs.
## Finally, we use a weighted distance function. This calculates 
### the distance between all image points and all gal points. 
### Selects the GAL point nearest each image point.
### Takes the _distance_ parameter (we're using 7 pixels) and if the GAL-Image point distance is less than our distance param, we use the following {noformat}f=fitness
d = maximum distance
n = number of image points
dn = distance from image point to nearest GAL point{noformat}
!fitnessfn.gif!]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_|#extraction]
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3){code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png")){code}


]]></property>
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<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment. The basic algorithm works as follows:

h2. The Genetic Algorithm

The basic building block of our genetic algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [linear transform|https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala] needed to rotate, scale, and align the GAL to the image and apply this to all the points in the GAL file.
# Calculate a fitness for the match between the image and GAL points. This fitness is actually a mutlipart evalucation
## First check that all the transformed GAL points are within the bounds of the image. If they are not we evaluate this match as _unfit_.
## Second, we check that the GAL points have not collapsed by calculating the most common distance between nearest neighbors. Then we check to see that this distance less than the maximum distance between image point pairs and greater then the minimum distance between point pairs.
## Finally, we use a weighted distance function. This calculates 
### the distance between all image points and all gal points. 
### Selects the GAL point nearest each image point.
### Takes the _distance_ parameter (we're using 7 pixels) and if the GAL-Image point distance is less than our distance param, we use the following {noformat}f  = fitness
d  = maximum distance
n  = number of image points
dn = distance from image point to nearest GAL point{noformat}
!fitnessfn.gif!]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_|#extraction]
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3){code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png")){code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just grab the upper left corner (in image space, where the upper left is the origin 90,0)
]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_|#extraction]
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3){code}

h1. {anchor:extraction}GAL Feature Extraction

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. The single GAL file defines multiple filters 
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("Amy_gal.png")){code}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_|#extraction]
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3){code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our print uses non-standard files. So while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("Amy_gal.png")){code}


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<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.

June 26 - continues to run, but lost internet access due to an unknown networking error.

h3. {color:#ff00ff}So. California Deployment of ESP-Gordon / NEO{color}

Aug 30 \-\- Haul instrument and gear in trailer and MBARI van to deploy on OCSD R/V Nerissa.  Calm seas, hot weather, instrument in \~10:30am.  Gordon w/PCR, CTD, ISUS, cell-phone modem (T-Mobile).  Sewage diversion to begin Sep 11, 2012. Machine located at 33.59703 \-117.94623.&nbsp; Divers from Orange County Sheriff's dept.

Kevan collecting data here: [http://www.stanford.edu/~kevany/ESP/].

Sep 14-noticed CTD battery draining faster than expected because of optode.&nbsp; Also, ATV encoder in MFB&nbsp; kept returning 511, which is 2**9-1&nbsp; meaning all bits are stuck high--typical way they fail.&nbsp; Stopped PCR, continued SHA, but with dead CTD no contextual data to adaptive sample off of.&nbsp; Decision to flip for NEO on Sep 26.

Sep 26\-\-recovered ESP-Gordon and swapped both batteries and ESP-Neo.&nbsp; Also changed CTD so now no optode (O2) measurments.&nbsp; One power cable fizzed away.&nbsp; Connector on pickle jar loose.&nbsp; But NEO now running well. Skipper gave deployment coordinates of 33 35.829 &nbsp; \-117 56.759.&nbsp; Xeos says&nbsp; 33.59702 \-117.94604.&nbsp; Water depth 18m.&nbsp; CTD/can depth=6.3m.&nbsp; Divers from LBAoP\-\-Eric Castillo and Steve Lang.

Oct 16\-\-Recovered ESP-Neo.&nbsp; Divers from LBAoP\-\-Steve Lang and Veronica Anderson.

h3. {color:#ff00ff}Fall CANON--Drifter with ESP-Moe / Moe{color}

WF leaves MBARI Sept 10.&nbsp; Moe with PCR, ISUS, CTD, PAR, and buoy has downward ADCP.&nbsp; Roman and Julie R. on ship.

Moe went into water Sep 11. First phase slated for 6pm.

Pulled Sep 17 (10:30am).&nbsp; E/M cable started flaking out either due to connector or bad ethernet extender.&nbsp; Decision to end mission unrelated to this. ]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_|#extraction]
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3){code}

h1. {anchor:extraction}GAL Feature Extraction

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. The single GAL file defines multiple filters 


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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser ]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_|#extraction]
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3){code}

h1. {anchor:extraction}GAL Feature Extraction

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. The single GAL file defines multiple filters 
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = GeneArrayIOServiceImpl.readArrayDescription((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("Amy_gal.png")){code}


]]></property>
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<property name="body"><![CDATA[[G3 Process Diagrams|^G3process-04-12-12.pptx]Revised: April 12, 2012

[Modular Cartridge Diagrams|^G3 Modular Cartridge 04-30-12.pptx]Revised: April 30, 2012]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_|#extraction]
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3){code}

h1. {anchor:extraction}GAL Feature Extraction



]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 2 things:
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!
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<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment. The basic algorithm works as follows:

For the alignment, our genetic algorithm uses a chromosome compose

The basic building block of our genetic algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points (where a point is an x, y pair in image pixel coordinates)
]]></property>
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<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment. The basic algorithm works as follows:

For the alignment, our genetic algorithm uses a chromosome compose

The basic building block of our genetic algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points (where a point is an x, y pair in image pixel coordinates). Only 2 points are actually used, but the 3rd point would be useful if we ever need to run an affine transform instead of a geometric transform.
]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.
#*
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<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment. The basic algorithm works as follows:

h2. The Genetic Algorithm

The basic building block of our genetic algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a geometric transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching
]]></property>
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<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.

June 26 - continues to run, but lost internet access due to an unknown networking error.

h3. {color:#ff00ff}Diversion Experiment; So. California Deployment of ESP-Gordon / NEO{color}

Aug 30 \-\- Haul instrument and gear in trailer and MBARI van to deploy on OCSD R/V Nerissa.  Calm seas, hot weather, instrument in \~10:30am.  Gordon w/PCR, CTD, ISUS, cell-phone modem (T-Mobile).  Sewage diversion to begin Sep 11, 2012. Machine located at 33.59703 \-117.94623.&nbsp; Divers from Orange County Sheriff's dept.

Kevan collecting data here: [http://www.stanford.edu/~kevany/ESP/].

Sep 14-noticed CTD battery draining faster than expected because of optode.&nbsp; Also, ATV encoder in MFB&nbsp; kept returning 511, which is 2**9-1&nbsp; meaning all bits are stuck high--typical way they fail.&nbsp; Stopped PCR, continued SHA, but with dead CTD no contextual data to adaptive sample off of.&nbsp; Decision to flip for NEO on Sep 26.

Sep 26--recovered ESP-Gordon and swapped both batteries and ESP-Neo.&nbsp; Also changed CTD so now no optode (O2) measurments.&nbsp; One power cable fizzed away.&nbsp; Connector on pickle jar loose.&nbsp; But NEO now running well. Skipper gave deployment coordinates of 33 35.829 &nbsp; \-117 56.759.&nbsp; Xeos says&nbsp; 33.59702 \-117.94604.&nbsp; Water depth 18m.&nbsp; CTD/can depth=6.3m.&nbsp; Divers from LBAoP--Eric Castillo and Steve Lang.

Oct 16--Recovered ESP-Neo.&nbsp; Divers from LBAoP--Steve Lang and Veronica Anderson.

h3. {color:#ff00ff}Fall CANON--Drifter with ESP-Moe / Moe{color}

WF leaves MBARI Sept 10.&nbsp; Moe with PCR, ISUS, CTD, PAR, and buoy has downward ADCP.&nbsp; Roman and Julie R. on ship.

Moe went into water Sep 11. First phase slated for 6pm.

Pulled Sep 17 (10:30am).&nbsp; E/M cable started flaking out either due to connector or bad ethernet extender.&nbsp; Decision to end mission unrelated to this. ]]></property>
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<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment. The basic algorithm works as follows:

h2. The Genetic Algorithm

The basic building block of our genetic algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala|linear transform] needed to rotate, scale, and align the GAL to the image. ]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 2 things:
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.

]]></property>
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<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment. The basic algorithm works as follows:

h2. The Genetic Algorithm

The basic building block of our genetic algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a geometric transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

The basic goal of the genetic algorithm is to take 2 points from the GAL and line calculate the linear transform needed to rotate, scale, and align them to 2 points on the image. ]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching
]]></property>
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<id name="id">19071564</id>
<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment. The basic algorithm works as follows:

h2. The Genetic Algorithm

The basic building block of our genetic algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [linear transform|https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala] needed to rotate, scale, and align the GAL to the image. ]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_|#extraction]
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
{code}
List<GALPoint> allPoints = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allPoints, 12500);
{code}
]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_|#extraction]
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3){code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png")){code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
]]></property>
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<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment. The basic algorithm works as follows:

h2. The Genetic Algorithm

The basic building block of our genetic algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [linear transform|https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala] needed to rotate, scale, and align the GAL to the image and apply this to all the points in the GAL file.
# Calculate a fitness for the match between the image and GAL points. This fitness is actually a mutlipart evalucation
## First check that all the transformed GAL points are within the bounds of the image. If they are not we evaluate this match as _unfit_.
## Second, we check that the GAL points have not collapsed by calculating the most common distance between nearest neighbors. Then we check to see that this distance less than the maximum distance between image point pairs and greater then the minimum distance between point pairs.
## Finally, we use a weighted distance function. This calculates the distance between all image points and all gal points. 
]]></property>
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</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">9830970</id>
<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_|#extraction]
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}
]]></property>
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<id name="id">19071568</id>
<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment. The basic algorithm works as follows:

h2. The Genetic Algorithm

The basic building block of our genetic algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [linear transform|https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala] needed to rotate, scale, and align the GAL to the image and apply this to all the points in the GAL file.
# Calculate a fitness for the match between the image and GAL points. This fitness is actually a mutlipart evalucation
## First check that all the transformed GAL points are within the bounds of the image. If they are not we evaluate this match as _unfit_.
## Second, we check that the GAL points have not collapsed by calculating the most common distance between nearest neighbors. Then we check to see that this distance less than the maximum distance between image point pairs and greater then the minimum distance between point pairs.
## Finally, we use a weighted distance function. This calculates 
### the distance between all image points and all gal points. 
### Selects the GAL point nearest each image point.
### Takes the _distance_ parameter (we're using 7 pixels) and if the GAL-Image point distance is less than our distanc param, we use: [!fitnessfn.gif!]]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071567</id>
<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment. The basic algorithm works as follows:

h2. The Genetic Algorithm

The basic building block of our genetic algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [linear transform|https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala] needed to rotate, scale, and align the GAL to the image and apply this to all the points in the GAL file.
# Calculate a fitness for the match between the image and GAL points. This fitness is actually a mutlipart evalucation
## First check that all the transformed GAL points are within the bounds of the image. If they are not we evaluate this match as _unfit_.
## Second, we check that the GAL points have not collapsed by calculating the most common distance between nearest neighbors. Then we check to see that this distance less than the maximum distance between image point pairs and greater then the minimum distance between point pairs.
## Finally, we use a weighted distance function. This calculates 
### the distance between all image points and all gal points. 
### Selects the GAL point nearest each image point.
### Takes the _distance_ parameter (we're using 7 pixels) and if the GAL-Image point distance is less than our distanc param, we use: {noformat} distance - point distance.
]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071570</id>
<property name="body"><![CDATA[h2. Overview

Once the points of interest are extracted from both the GAL file and image our next goal is to align the GAL points to those on the image. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment. The basic algorithm works as follows:

h2. The Genetic Algorithm

The basic building block of our genetic algorithm is a _chromosome_. Our chromosome encodes information that represents 3 points, where a point is an x, y pair in image pixel coordinates. Only two points are used, but the 3rd point would be useful if we ever need to run an affine transform instead of a linear transform. An individual chromosome is created as follows:

{code}
import org.mbari.esp.ia.geometry.Point2D
import org.mbari.esp.ia.ga.PointChromosome

val p0 = Point2D(10, 10)
val p1 = Point2D(20, 20)
val p2 = Point2D(30, 30)
val chromosome = PointChromosome(p0, p1, p2)
{code}

The basic goal of the genetic algorithm is to take 2 points from the GAL and match them to the corresponding 2 points on the image. To achieve this we do the following:
# Calculate the [linear transform|https://bitbucket.org/hohonuuli/esp-image-analysis/src/859c1f31ba5d/src/main/scala/org/mbari/esp/ia/ga/RigidTransform.scala] needed to rotate, scale, and align the GAL to the image and apply this to all the points in the GAL file.
# Calculate a fitness for the match between the image and GAL points. This fitness is actually a mutlipart evalucation
## First check that all the transformed GAL points are within the bounds of the image. If they are not we evaluate this match as _unfit_.
## Second, we check that the GAL points have not collapsed by calculating the most common distance between nearest neighbors. Then we check to see that this distance less than the maximum distance between image point pairs and greater then the minimum distance between point pairs.
## Finally, we use a weighted distance function. This calculates 
### the distance between all image points and all gal points. 
### Selects the GAL point nearest each image point.
### Takes the _distance_ parameter (we're using 7 pixels) and if the GAL-Image point distance is less than our distanc param, we use: !fitnessfn.gif!]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want)
]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

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<property name="body"><![CDATA[h2. Overview

After the point features are extracted we need to align the GAL points to the image points. We use a [genetic algorithm|http://en.wikipedia.org/wiki/Genetic_algorithm] to do the alignment]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# [Extracting the intensities values from the filter image (_Data Extraction_)|#data]

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}

h1. {anchor:data}Data Extraction

Without being able to align the filter image with the GAL points, it's impossible to:
# Associate a spot with it's content
# Accurately and reliable extract all spots of interest.

Here's a few examples of just trying to extract spots from an image:

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<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns.
\\

h4.


h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5


May 2 \-\- Deploy ESP-Chris
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}
]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. For the test image, I was able modify the transform to accuratly align rotation and translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Filter Subregion}!ImageRegistrationTest01-test01-bestR2.png!{info}

{info:title=Log-polar Transform of Filter Subregion!ImageRegistrationTest01-test01-bestR2p.png!{info}

]]></property>
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<id name="id">9830979</id>
<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.
#* [^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]
]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">9830986</id>
<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!{info}

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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# Extracting the intensities values from the filter image

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Filter Subregion}!ImageRegistrationTest01-test01-bestR2.png!{info}

{info:title=Log-polar Transform of Filter Subregion}!ImageRegistrationTest01-test01-bestR2p.png!{info}

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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# [Extracting the intensities values from the filter image (_Data Extraction_)|#data]

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}

h1. {anchor:data}Data Extraction

Without being able to align the filter image with the GAL points, it's impossible to:
# Associate a spot with it's content
# Accurately and reliable extract all spots of interest.

Here's a few examples of just trying to extract spots from an image:
{info:title=The Good}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_3-40s.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1.tif.png!
{info}
{info:title=The Bad}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-40s.tif.png!
{info}
{info:title=The Ugly}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}

h1. Summary

The only hurdle that needs to be overcome at this point is [pattern matching/image registration|#matching]

Here are the signficant hurdles for _pattern matching/image regsitration_:
# Reliably extracting spots from the filter image
#* In my test images, I was only able to extract all spots in one image using thresholding techniques.
#* Another technique to try would be edge detection. This may be problematic in noisier images though. 
# Dealing with symmetry in the spot layout, this confounds most image registration techniques.
#* It would be great if I could get some *key spots* that I can reliably detect and differentiate from the other spots. For example, 2 spots that are near the edge of the disk. If I could extract those then, I would be able to easily register the GAL file with the image. As an example, look at the image above an notice the single spot near the edge of the disk. If we had 2 of those on that image it would make my life much simpler!! ;-)

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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# CVS client

h3. Steps to build and run

# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:
{code}
cvs checkout ESP/gen2/software
{code}
# &nbsp; (or if you want a branch like GUI2 (with head for anything not on branch \-f )
{code}
cvs checkout -f -r GUI2 ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# You must apply some patches by copying the *.rb files (about 4) from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/{version}
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# [Extracting the intensities values from the filter image (_Data Extraction_)|#data]

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}

h1. {anchor:data}Data Extraction

Without being able to align the filter image with the GAL points, it's impossible to:
# Associate a spot with it's content
# Accurately and reliable extract all spots of interest.

Here's a few examples of just trying to extract spots from an image:
{info:title=The Good}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_3-40s.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1.tif.png!
{info}
{info:title=The Bad}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-40s.tif.png!
{info}
{info:title=The Ugly}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}

h1. Summary

The only hurdle that needs to be overcome at this point is [pattern matching/image registration|#matching]

Here are the signficant hurdles for _pattern matching/image regsitration_:
# Reliably extracting spots from the filter image
#* In my test images, I was only able to extract all spots in one image using thresholding techniques.
#* Another technique to try would be edge detection. This may be problematic in noisier images though. 
# Dealing with symmetry in the spot layout, this confounds most image registration techniques.
#* It would be great if I could get some *key spots* that I can reliably detect and differentiate from the other spots. For example, 2 spots that are near the edge of the disk. If I could extract those then, I would be able to easily register the GAL file with the image.

]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

{note}
As of 4/1/2011, this appears to no longer work for the Mac.
{note}

h3. Prerequisites

# CVS client
# gcc
# yacc

h3. Steps to build and run

# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:
{code}
cvs checkout ESP/gen2/software
{code}
# &nbsp; (or if you want a branch like GUI2 (with head for anything not on branch \-f )
{code}
cvs checkout -f -r GUI2 ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.
{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This un-tars the files from the ../snapshot-1.6.tar.gz file into the directory you are in without overwriting the existing files (which are the patches).
# Now run the configure command
{code}
./configure
{code}
# Now run make.
{code}
make
{code}
# If all goes well, ruby will have built and you can install by running this as 'root'.
{code}
make install
{code}
# After that, ruby should be ready to go and if you type
{code}
ruby --version
{code}
You should see something like:
{code}
ruby 1.6.8-mbari7/0x4770 (2009-1-19) [i686-linux]
{code}
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username

{noformat}
copy *.rb from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/{version}
{noformat}]]></property>
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<id name="id">19071525</id>
<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

{note}
As of 4/1/2011, this appears to no longer work for the Mac.
{note}

h3. Prerequisites

# CVS client
# gcc
# yacc

h3. Steps to build and run

# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:
{code}
cvs checkout ESP/gen2/software
{code}
# &nbsp; (or if you want a branch like GUI2 (with head for anything not on branch \-f )
{code}
cvs checkout -f -r GUI2 ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.
{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This un-tars the files from the ../snapshot-1.6.tar.gz file into the directory you are in without overwriting the existing files (which are the patches).
# Now run the configure command
{code}
./configure
{code}
# Now run make.
{code}
make
{code}
# If all goes well, ruby will have built and you can install by running this as 'root'.
{code}
make install
{code}
# After that, ruby should be ready to go and if you type
{code}
ruby --version
{code}
You should see something like:
{code}
ruby 1.6.8-mbari7/0x4770 (2009-1-19) [i686-linux]
{code}
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username]]></property>
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<property name="body"><![CDATA[h2. For the developers

# [Getting the source|http://oceana/projects/esp/source-repository.html]
# [Opening in an IDE]]]></property>
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<id name="id">19071538</id>
<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns.\\

h4.


h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI

May 2 \-\- Deploy ESP-Chris
\\]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# [Extracting the intensities values from the filter image (_Data Extraction_)|#data]

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}

h1. {anchor:data}Data Extraction

Without being able to align the filter image with the GAL points, it's impossible to:
# Associate a spot with it's content
# Accurately and reliable extract all spots of interest.

Here's a few examples of just trying to extract spots from an image:
{info:title=The Good}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_3-40s.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1.tif.png!
{info}
{info:title=The Bad}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-40s.tif.png!
{info}
{info:title=The Ugly}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}

]]></property>
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<id name="id">19071537</id>
<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#cc00ff}March 19{color}\--ESP Sea-van leaves MBARI for Oakland

{color:#cc00ff}March 20{color} \-\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight. ]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">9830996</id>
<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# [Extracting the intensities values from the filter image (_Data Extraction_)|#data]

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}

h1. {anchor:data}Data Extraction

Without being able to align the filter image with the GAL points, it's impossible to:
# Associate a spot with it's content
# Accurately and reliable extract all spots of interest.

Here's a few examples of just trying to extract spots from an image:
{info:title=The Good}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_3-40s.tif.png!
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1.tif.png!
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-40s.tif.png!
{info}
{info:title=The Bad}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2.tif.png!
{info}
{info:title=The Ugly}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}

]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">9830995</id>
<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# [Extracting the intensities values from the filter image (_Data Extraction_)|#data]

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}

h1. {anchor:data}Data Extraction

Without being able to align the filter image with the GAL points, it's impossible to:
# Associate a spot with it's content
# Accurately and reliable extract all spots of interest.

Here's a few examples of just trying to extract spots from an image:
{info:title=The Good}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_3.tif.png!
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1.tif.png!
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-40s.tif.png!
{info}
{info:title=The Bad}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2.tif.png!
{info}
{info:title=The Ugly}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}

]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">9831002</id>
<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# [Extracting the intensities values from the filter image (_Data Extraction_)|#data]

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}

h1. {anchor:data}Data Extraction

Without being able to align the filter image with the GAL points, it's impossible to:
# Associate a spot with it's content
# Accurately and reliable extract all spots of interest.

Here's a few examples of just trying to extract spots from an image:
{info:title=The Good}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_3-40s.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1.tif.png!
{info}
{info:title=The Bad}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-40s.tif.png!
{info}
{info:title=The Ugly}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}

h1. Summary

The only hurdle that needs to be overcome at this point is [pattern matching/image registration|#matching]

Here are the signficant hurdles for _pattern matching/image regsitration_:
# Reliably extracting spots from the filter image
#* In my test images, I was only able to extract all spots in one image using thresholding techniques.
#* Another technique to try would be edge detection. This may be problematic in noisier images though. 
# Dealing with symmetry in the spot layout, this confounds most image registration techniques.

]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">9831000</id>
<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# [Extracting the intensities values from the filter image (_Data Extraction_)|#data]

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}

h1. {anchor:data}Data Extraction

Without being able to align the filter image with the GAL points, it's impossible to:
# Associate a spot with it's content
# Accurately and reliable extract all spots of interest.

Here's a few examples of just trying to extract spots from an image:
{info:title=The Good}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_3-40s.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1.tif.png!
{info}
{info:title=The Bad}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-40s.tif.png!
{info}
{info:title=The Ugly}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}

h1. Summary

The only hurdle that needs to be overcome at this point is [pattern matching/image registration|#matching]

Here are the signficant hurdles for _pattern matching/image regsitration_:
# Reliably extracting spots from the filter image
#* In my test images, I was only able to extract all spots in one image.
# Dealing with symmetry in the spot layout, this confounds most image registration techniques.

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<property name="body"><![CDATA[For several aspects of the ESP GUI application, the application will have to have an associated user, which will, in turn, belongs to specifics groups.  The reason for this is that we do not want the application to allow any user to do all things in the ESP GUI.  For example:

# Maybe you want to limit users to read-only.
# Certain users can create mission scripts for certain ESP instrument
# Certain users can delete deployment information.
# etc.

In order to enable this type of access control, the Java SE security infrastructure was utilized in the GUI development.

Resources:

# [Java SE Security|http://www.oracle.com/technetwork/java/javase/tech/index-jsp-136007.html]
# [Java SE Security Overview|http://download.oracle.com/javase/7/docs/technotes/guides/security/overview/jsoverview.html]]]></property>
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<property name="body"><![CDATA[For several aspects of the ESP GUI application, the application will have to have an associated user, which will, in turn, belongs to specifics groups.  The reason for this is that we do not want the application to allow any user to do all things in the ESP GUI.  For example:

# Maybe you want to limit users to read-only.
# Certain users can create mission scripts for certain ESP instrument
# Certain users can delete deployment information.
# etc.

In order to enable this type of access control, the Java SE security infrastructure was utilized in the GUI development.

Resources:

# [Java SE Security|http://www.oracle.com/technetwork/java/javase/tech/index-jsp-136007.html]
# [Java SE Security Overview|http://download.oracle.com/javase/7/docs/technotes/guides/security/overview/jsoverview.html]
# [JAAS Reference Guide|http://download.oracle.com/javase/6/docs/technotes/guides/security/jaas/JAASRefGuide.html]
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<property name="body"><![CDATA[h4.


h4. {color:#ff00cc}SCRIPPS-Lab Run \-\- ESP-Waldo{color}

*&nbsp;April 27, 2015*

Roman delivers ESP Waldo to Andy Allen's lab at CVGI.&nbsp; Idea was to collect archived sample twice/week for \~6 months to test longevity issues with filters.

mid-June, instrument started losing comms to elevator dwarf.&nbsp; Roman sent down to replace dwarf on June 29-30. Re-canned and restarted mission.

RECOVERY

Roman recovers ESP-Waldo October 6, 2015.

h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce. Divers: Kim R., Paul C.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

Divers: Paul C., Jeff Sevadjian

{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload. Divers: Eric R, Jeff Sevadjian
\\

h4. {color:#ff00cc}1st MAKAI flight w 5 cartridges{color}

*July 22, 2015*

Flew triangle pattern after launch.&nbsp; Makai found chlorophyll feature, and we fired two cartridges while flying through.&nbsp; First cartridge may have had sticky valve and stayed in by-pass (filtered 1L in \~20 minutes; too fast).&nbsp; Second cartridge seemed to have worked.

Some issues with ESP not communicating it was on, and then LRAUV not turning it on.&nbsp; Went to recover vehicle late July 23, but did not surface until mission timed-out, after we were already ashore.&nbsp; That was when we discovered the comms issues.&nbsp; Fixed one, tried to fire during a 'night operation' Thursday evening.&nbsp; Discovered Friday morning a second comms issues, which was fixed, and fired the 3 samples during day on Friday, July 24.&nbsp; Did keep-station all weekend, and recovered LRAUV early Monday morning (July 27).

Results:

1.&nbsp; Cartridge #1 bypassed 1L (toroid valve stuck; sea water ran through instrument in bypass mode; 7 minutes); flying through feature (chl=3.0 ug/l; 10.97m)

2. &nbsp; #2 filtered 815.8ml; flying through feature (11.03m; chl=3.3 ug/l; took 53 minutes)

3. &nbsp; #3 filtered 802.3ml;&nbsp; within feature (13.8m; chl=3.02 ug/l; took 51 minutes)

4. &nbsp; #4 filtered 759.6ml,&nbsp; above feature (7.1m; chl=1.11 ug/l; took 50 minutes)

5.&nbsp;&nbsp; #5 filtered 809.1ml,&nbsp; below feature (19.4m; chl=4.24 ug/l; took 51 minutes)

Excellent summary paper by Yanwu Zhang about what the LRAUV did during this deployment-\-[here|^Zhang_etal_chlpeak.pdf|Yanwu's paper].(check your download folder)

h4. {color:#ff00cc}SCRIPPS-Del Mar Mooring \-\- ESP-Waldo{color}

*&nbsp;November 12, 2015*

Roman and Scott drive down Nov 8 and work for the week to assemble mooring.&nbsp; Goes in water on the 12th (check ESP-Waldo channel on Slack for pictures).&nbsp; Setup has SCRIPPS modem as master mooring controller.&nbsp; when it sends command string to ESP, ESP and ESP-modem awake, which allows us to get into ESP for diagnosis and large data transfers.&nbsp; At end of sampling, ESP and it's modem goes to sleep.&nbsp; Currently (Dec 1) using [this|^ESP deploy _DelMar_sampling_127.xlsx|Sampling schedule as of Dec 1] sampling schedule.

Dec 6, 2015

I2C error has stopped our sampling mission.&nbsp; ESP now providing only CTD updates.&nbsp; Brent's message:&nbsp; "The problem that surfaced first last Wednesday has recurred and is not going away this time.

Waldo's ESP host can access the sleepy microcontroller to get can status, etc., however, sleepy cannot access anything on the I2C bus."

Dec 14, 2015

I2C bus was back online\!&nbsp; Instrument had been left 'on' since last communications, and had some rough weather over this weekend.&nbsp; Brent was able to get in and unstick the hand then take a 'flawless' sample.&nbsp; Will see how she works in four days...
\\

\\]]></property>
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<property name="body"><![CDATA[This is the documentation to detail out the design of the state representation interface between the GUI application and the instrument itself.  This interface will allow the GUI (and other applications) to get information about the current state of the various components of the ESP.

Some details about the interface:

# The ESP application (server) shall listen on a fixed TCP socket.
# Any number clients can connect to this socket, each thereby opening a separate, private, bidirectional, ASCII connection to the ESP server.
# The server will respond to the following client commands:
##  List all available states
### Each state is identified by a short ASCII(symbolic) name. Metadata shall include:
#### Description  e.g.  Storage carousel
#### sprintf format string  e.g.  %.2fml
#### range  (min and max expected values)
#### hardware failures may cause reported values to be out of range
## Subscribe to updates on (only) the specified states
{note}
This limits subsequent state updates to just those listed by their symbolic names. This message is required because it determines the ordering of states in vectors described below.
{note}
## Refresh all subscribed states
{note} 
All the subscribed states are sent to the client in the order in which they were listed in the most recent subscribe message.
{noformat}
<timestamp?  seconds since epoch??>
<new value[0]>
<new value[1]>
...
<new value[n-1]>
{noformat}
where n is the number of states subscribed.  This establishes a baseline from which subsequent state changes are reported.
{note}
## Request C more changed state updates at maximum rate one per t tenths of seconds.
{note}
* The client tells the server it is ready to receive C more state change responses and that the server may emit these at a rate no faster than one every t tenths of a second.
* A client wishing to continuously monitor state should send a new request shortly *before*  the last update (as allowed by the previous request) has been received. If C is kept small (say 10 or so), this mechanism will ensure that update messages don't back up on the networking queue, while avoiding paying any network latency penalty.  (Similar to TCP's sliding window mechanism)
* The client can stop updates by requesting 0 more at some arbitrary rate.
* Only those states whose values changed since the last update will be sent
* Format will be a list of elements, each of the form:
{noformat}
<index>,<new value>
{noformat}
where:
* index = an integer from 0 to n-1 where n is the number of subscribed states
* new value = number conforming to the state's sprintf format string (note that the unit suffix will be omitted, i.e. 0.2 not 0.2ml)
{note}

{note:title=Notes for Brent}
Normally, all I2C messages between the Linux host and the dwarves are logged. However, this protocol will require continuous polling of all the subscribed dwarves' raw positions.  Nothing else currently does anything like this (by design! :-). Clearly, such messages should not be logged.  Further, it may be necessary to add an I2C message to the dwarf firmware that queries raw position only.  The existing full status poll message returns lots of extraneous engineering info like velocity, electrical current, etc.
{note}]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]
# [Feb 16]
# Feb 23 \-\- Oceans Mtg., Portland
# [Mar 2]
# [Mar 9]
# Mar 16 \-\- Jim in S. Cal scouting.  John Ryan ran mtg.
# Mar 23
# Mar 30
# Apr 6 \-\- canceled in preparation for M0 deployment
# Apr 13
# Apr 20
# Apr 27 \--AbSciCon, League City TX
# [May 4]
# [May 11]
# [May 18]
# [Aug 24]
# [Sep 14]
# [Sep 21]
# Sep 28 \-\- Network deployment.&nbsp; no mtg
# Oct 5
# Oct 12
# Oct 19
# Oct 26 \-\- Chris S. @ WHOI, Jim at PICES
# [Nov 2]
# [Nov 9]]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]
# [Feb 16]
# Feb 23 \-\- Oceans Mtg., Portland
# [Mar 2]
# [Mar 9]
# Mar 16 \-\- Jim in S. Cal scouting.  John Ryan ran mtg.
# Mar 23
# Mar 30
# Apr 6 \-\- canceled in preparation for M0 deployment
# Apr 13
# Apr 20
# Apr 27 \--AbSciCon, League City TX
# [May 4]
# [May 11]
# [May 18]
# [Aug 24]
# [Sep 14]]]></property>
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<property name="body"><![CDATA[Present:&nbsp;&nbsp; Vanessa, Jim, Roman, Bill U., Chris S., Scott, Brent, John R., Chris P., Doug, Elif, Liz O.
Absent: Julie

{color:#3300ff}1. Items:{color}\\
* {color:#3300ff}BioSpace Deployment{color}
** {color:#000000}Message from Aaron (Zephyr skipper) was he'd like to do 3 in one day.&nbsp; This crowds the boat and is not ideal, but we may go with this if we have divers.&nbsp; Still planning....{color}
** {color:#000000}Precruise has crew being Roman, Scott, Vanessa, Bruce K.{color}
** &nbsp;

* {color:#3300ff}D-ESP Plan{color}
** New IEP pump to arrive by end of week.&nbsp; Doug has \~3.5 weeks to install, test, and checkout.
** Plan is to load reagents Oct 21.&nbsp; From then on the ball should be kept at 16C, which means van at 10C w/ sphere heater on.
** Plan is to try and run 3 full phases as a checkout.
** Julie has had some trouble with IPC on the MFB;&nbsp; it's internally  consistent in it's Ct, but Ct's are different depending on if sample is  run through the core or stand-alone.&nbsp; Julie has been hammering on this  problem with advice from Chris P (on the WF Canon cruise).&nbsp; Might be a  bad pull from PP1 pigtail, which has been replaced.&nbsp; She is also trying a  'better' IPC mixture.
** Julie will continue to work on getting the instrument working; she  leaves on a trip Thursday PM, and should not worry about canning, as  we'll take care that issue.

* {color:#3300ff}Bruce{color}
** Roman saw that Bruce failed the short DA yesterday, but discovered  the puck heater was too hot to touch.  Seems to be a temperature  feedback issue.  Will investigate with Scott today.

h5. Missions for Biospace

* From Aug 9, Roman had notes stating we'd run 15 HAB/DA, 4 Bac, 3 Larv.
* julie/vanessa setting up Moe.
* all mission plans to be finished by Friday (17th) for discussion next Tuesday.
* Jim will contact Spyglass to find out where they are with the new puck cleaning.]]></property>
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<property name="body"><![CDATA[h3. Distribution list as of 4 Nov 2010:
\\
\\

|| MFB || PCR Module # || on Core || who gets? || ||
| tombstone | 5 \\ | NEO \\ | MBARI | |
| MFB1 | 1 | Moe | MBARI | |
| MFB2 | 12 \\ | \\ | {color:#006699}slated for{color} CMORE (UCSC) | |
| MFB3 | 4 | Gordon | MBARI | |
| MFB4 | 7 \\ | Betty | MBARI | |
| MFB5 | \\ | | \\ | |
| MFB6 | 8 \\ | | At SCCWRP (S. Cal) | \\ |
| MFB7 | | | {color:#006699}slated for{color} Harvard/Girgius | |
| MFB8 | none | | At Stony Brook, NY (Harbans Dhadwal) | |
| MFB9 | 13 \\ | | At Caltech/Orphan | |
| MFB10 | 11 | | At Stanford (Chris Francis) | |
| {color:#000000}&nbsp;MFB11{color} | 14 \\ | | MBARI | \\ |
| | | | | |
| | Spares:&nbsp; none | | | |
| | \\ | | | |
| | Broken?: | | | |
| | 3 | | was originally on Tombstone, but moved #9 there for M0 deployment. Not enough sensitivity.&nbsp; \\ | |
| | 10 | | removed from MFB6.&nbsp; Bleach leak caused flakey connector. \\ | |
| | 9 | | removed from tombstone.&nbsp; Erratic diode readings \\ | |]]></property>
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<property name="body"><![CDATA[h3. Distribution list as of 4 Nov 2010:

\\
\\
|| MFB || PCR Module # || on Core || who gets? || ||
| tombstone | 5 \\ | NEO \\ | MBARI | |
| MFB1 | 1 | Moe | MBARI | |
| MFB2 | 12 \\ | \\ | {color:#006699}slated for{color} CMORE (UCSC) | |
| MFB3 | 4 | Gordon | MBARI | |
| MFB4 | 7 \\ | Betty | MBARI | |
| MFB5 | \\ | | \\ | |
| MFB6 | 8 \\ | | At SCCWRP (S. Cal) | \\ |
| MFB7 | | | {color:#006699}slated for{color} Harvard/Girgius | |
| MFB8 | none | | At Stony Brook, NY (Harbans Dhadwal) | |
| MFB9 | 13 \\ | | At Caltech/Orphan | |
| MFB10 | 11 | | At Stanford (Ali Boehm's lab) | |
| {color:#000000}&nbsp;MFB11{color} | 14 \\ | | MBARI | \\ |
| | | | | |
| | Spares:&nbsp; none | | | |
| | \\ | | | |
| | Broken?: | | | |
| | 3 | | was originally on Tombstone, but moved #9 there for M0 deployment. Not enough sensitivity.&nbsp; \\ | |
| | 10 | | removed from MFB6.&nbsp; Bleach leak caused flakey connector. \\ | |
| | 9 | | removed from tombstone.&nbsp; Erratic diode readings \\ | |]]></property>
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<property name="body"><![CDATA[h4.


h4. {color:#ff00cc}SCRIPPS-Lab Run \-\- ESP-Waldo{color}

*&nbsp;April 27, 2015*

Roman delivers ESP Waldo to Andy Allen's lab at CVGI.&nbsp; Idea was to collect archived sample twice/week for \~6 months to test longevity issues with filters.

mid-June, instrument started losing comms to elevator dwarf.&nbsp; Roman sent down to replace dwarf on June 29-30. Re-canned and restarted mission.

RECOVERY

Roman recovers ESP-Waldo October 6, 2015.

h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce. Divers: Kim R., Paul C.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

Divers: Paul C., Jeff Sevadjian

{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload. Divers: Eric R, Jeff Sevadjian
\\

h4. {color:#ff00cc}1st MAKAI flight w 5 cartridges{color}

*July 22, 2015*

Flew triangle pattern after launch.&nbsp; Makai found chlorophyll feature, and we fired two cartridges while flying through.&nbsp; First cartridge may have had sticky valve and stayed in by-pass (filtered 1L in \~20 minutes; too fast).&nbsp; Second cartridge seemed to have worked.

Some issues with ESP not communicating it was on, and then LRAUV not turning it on.&nbsp; Went to recover vehicle late July 23, but did not surface until mission timed-out, after we were already ashore.&nbsp; That was when we discovered the comms issues.&nbsp; Fixed one, tried to fire during a 'night operation' Thursday evening.&nbsp; Discovered Friday morning a second comms issues, which was fixed, and fired the 3 samples during day on Friday, July 24.&nbsp; Did keep-station all weekend, and recovered LRAUV early Monday morning (July 27).

Results:

1.&nbsp; Cartridge #1 bypassed 1L (toroid valve stuck; sea water ran through instrument in bypass mode; 7 minutes); flying through feature (chl=3.0 ug/l; 10.97m)

2. &nbsp; #2 filtered 815.8ml; flying through feature (11.03m; chl=3.3 ug/l; took 53 minutes)

3. &nbsp; #3 filtered 802.3ml;&nbsp; within feature (13.8m; chl=3.02 ug/l; took 51 minutes)

4. &nbsp; #4 filtered 759.6ml,&nbsp; above feature (7.1m; chl=1.11 ug/l; took 50 minutes)

5.&nbsp;&nbsp; #5 filtered 809.1ml,&nbsp; below feature (19.4m; chl=4.24 ug/l; took 51 minutes)

Excellent summary paper by Yanwu Zhang about what the LRAUV did during this deployment-\-[here|^Zhang_etal_chlpeak.pdf|Yanwu's paper].(check your download folder)

h4. {color:#ff00cc}SCRIPPS-Del Mar Mooring \-\- ESP-Waldo{color}

*&nbsp;November 12, 2015*

Roman and Scott drive down Nov 8 and work for the week to assemble mooring.&nbsp; Goes in water on the 12th (check ESP-Waldo channel on Slack for pictures).&nbsp; Setup has SCRIPPS modem as master mooring controller.&nbsp; when it sends command string to ESP, ESP and ESP-modem awake, which allows us to get into ESP for diagnosis and large data transfers.&nbsp; At end of sampling, ESP and it's modem goes to sleep.&nbsp; Currently (Dec 1) using [this|^ESP deploy _DelMar_sampling_127.xlsx|Sampling schedule as of Dec 1] sampling schedule.

Dec 6, 2015

I2C error has stopped our sampling mission.&nbsp; ESP now providing only CTD updates.&nbsp; Brent's message:&nbsp; "The problem that surfaced first last Wednesday has recurred and is not going away this time.

Waldo's ESP host can access the sleepy microcontroller to get can status, etc., however, sleepy cannot access anything on the I2C bus."

&nbsp;


\\]]></property>
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<property name="body"><![CDATA[h4.


h4. {color:#ff00cc}SCRIPPS-Lab Run \-\- ESP-Waldo{color}

*&nbsp;April 27, 2015*

Roman delivers ESP Waldo to Andy Allen's lab at CVGI.&nbsp; Idea was to collect archived sample twice/week for \~6 months to test longevity issues with filters.

mid-June, instrument started losing comms to elevator dwarf.&nbsp; Roman sent down to replace dwarf on June 29-30. Re-canned and restarted mission.

RECOVERY

Roman recovers ESP-Waldo October 6, 2015.


h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce. Divers: Kim R., Paul C.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

Divers: Paul C., Jeff Sevadjian

{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload. Divers: Eric R, Jeff Sevadjian
\\

h4. {color:#ff00cc}1st MAKAI flight w 5 cartridges{color}

*July 22, 2015*

Flew triangle pattern after launch.&nbsp; Makai found chlorophyll feature, and we fired two cartridges while flying through.&nbsp; First cartridge may have had sticky valve and stayed in by-pass (filtered 1L in \~20 minutes; too fast).&nbsp; Second cartridge seemed to have worked.

Some issues with ESP not communicating it was on, and then LRAUV not turning it on.&nbsp; Went to recover vehicle late July 23, but did not surface until mission timed-out, after we were already ashore.&nbsp; That was when we discovered the comms issues.&nbsp; Fixed one, tried to fire during a 'night operation' Thursday evening.&nbsp; Discovered Friday morning a second comms issues, which was fixed, and fired the 3 samples during day on Friday, July 24.&nbsp; Did keep-station all weekend, and recovered LRAUV early Monday morning (July 27).

Results:

1.&nbsp; Cartridge #1 bypassed 1L (toroid valve stuck; sea water ran through instrument in bypass mode; 7 minutes); flying through feature (chl=3.0 ug/l; 10.97m)

2. &nbsp; #2 filtered 815.8ml; flying through feature (11.03m; chl=3.3 ug/l; took 53 minutes)

3. &nbsp; #3 filtered 802.3ml;&nbsp; within feature (13.8m; chl=3.02 ug/l; took 51 minutes)

4. &nbsp; #4 filtered 759.6ml,&nbsp; above feature (7.1m; chl=1.11 ug/l; took 50 minutes)

5.&nbsp;&nbsp; #5 filtered 809.1ml,&nbsp; below feature (19.4m; chl=4.24 ug/l; took 51 minutes)

Excellent summary paper by Yanwu Zhang about what the LRAUV did during this deployment-\-[here|^Zhang_etal_chlpeak.pdf|Yanwu's paper].(check your download folder)

h4. {color:#ff00cc}SCRIPPS-Del Mar Mooring \-\- ESP-Waldo{color}

*&nbsp;November 12, 2015*

Roman and Scott drive down Nov 8 and work for the week to assemble mooring.&nbsp; Goes in water on the 12th (check ESP-Waldo channel on Slack for pictures).&nbsp; Setup has SCRIPPS modem as master mooring controller.&nbsp; when it sends command string to ESP, ESP and ESP-modem awake, which allows us to get into ESP for diagnosis and large data transfers.&nbsp; At end of sampling, ESP and it's modem goes to sleep.&nbsp; Currently (Dec 1) using [this|^ESP deploy _DelMar_sampling_127.xlsx|Sampling schedule as of Dec 1] sampling schedule.

\\]]></property>
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<property name="body"><![CDATA[h4.


h4. {color:#ff00cc}SCRIPPS \-\- ESP-Waldo{color}

*&nbsp;April 27, 2015*

Roman delivers ESP Waldo to Andy Allen's lab at CVGI.&nbsp; Idea was to collect archived sample twice/week for \~6 months to test longevity issues with filters.

mid-June, instrument started losing comms to elevator dwarf.&nbsp; Roman sent down to replace dwarf on June 29-30. Re-canned and restarted mission

h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce. Divers: Kim R., Paul C.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

Divers: Paul C., Jeff Sevadjian

{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload. Divers: Eric R, Jeff Sevadjian
\\

h4. {color:#ff00cc}1st MAKAI flight w 5 cartridges{color}

*July 22, 2015*

Flew triangle pattern after launch.&nbsp; Makai found chlorophyll feature, and we fired two cartridges while flying through.&nbsp; First cartridge may have had sticky valve and stayed in by-pass (filtered 1L in \~20 minutes; too fast).&nbsp; Second cartridge seemed to have worked.

Some issues with ESP not communicating it was on, and then LRAUV not turning it on.&nbsp; Went to recover vehicle late July 23, but did not surface until mission timed-out, after we were already ashore.&nbsp; That was when we discovered the comms issues.&nbsp; Fixed one, tried to fire during a 'night operation' Thursday evening.&nbsp; Discovered Friday morning a second comms issues, which was fixed, and fired the 3 samples during day on Friday, July 24.&nbsp; Did keep-station all weekend, and recovered LRAUV early Monday morning (July 27).

Results:

1.&nbsp; Cartridge #1 bypassed 1L (toroid valve stuck; sea water ran through instrument in bypass mode; 7 minutes); flying through feature (chl=3.0 ug/l; 10.97m)

2. &nbsp; #2 filtered 815.8ml; flying through feature (11.03m; chl=3.3 ug/l; took 53 minutes)

3. &nbsp; #3 filtered 802.3ml;&nbsp; within feature (13.8m; chl=3.02 ug/l; took 51 minutes)

4. &nbsp; #4 filtered 759.6ml,&nbsp; above feature (7.1m; chl=1.11 ug/l; took 50 minutes)

5.&nbsp;&nbsp; #5 filtered 809.1ml,&nbsp; below feature (19.4m; chl=4.24 ug/l; took 51 minutes)

Excellent summary paper by Yanwu Zhang about what the LRAUV did during this deployment-\-[here|^Zhang_etal_chlpeak.pdf|Yanwu's paper].(check your download folder)]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


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<property name="body"><![CDATA[Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note that we have yet to make a full batch of high-volume snap pucks, but when we do, those will be labeled 1HV (top and bottom).

Here is who is doing our etching:

LaserMark
2109 O'Toole Ave. Ste S
San Jose, CA 95131
Phone 408 433-9333
Fax 408 433-9343
\\
\\

Here is what I have packed up for etching:
| Type | Top/bottom | Numbered | Amount | NOTE |
| WCR | Top | 040-079 | 40 | \\ |
| \\ | Bottom | 040-079 | 40 | \\ |
| LAF | Top | 040-078 | 39 | 1=Missing |
| \\ | Bottom | 040-078 | 39 | 1=Missing |
| SAF | Top | 040-075 | 36 | 4sent to Gregg D |
| \\ | Bottom | 040-075 | 36 | 4sent to Gregg D |
| SHT | Top | 080-159 | 80 | \\ |
| SH1 | Bottom | 080-159 | 80 | \\ |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 390 | \\ |
\\
\\

I also sent 1 WCR puck (top&bottom) as a font sample.&nbsp; When these come back I will pack up the ones that are to be re-numbered(SHT2000-079).&nbsp; I haven't received a quote yet but Laser Mark said about $2 each piece + shipping.\\

3/24/08

The SH1 tops that were misprinted are going to be sent out tomorrow to be re etched along with one of the LAF's that escaped detection last time:
| Type | Top/bottom | Numbered | Amount | NOTE |
| LAF | Top | 079 | 1 | Found the Lost 1\! |
| \\ | Bottom | 079 | 1 | \\ |
| SHT | Top | 000-079 | 80 | Old etching to be X'd out |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 82 | \\ |

That is all for now]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]
# [May 20]
# [May 27]
# June 3
# June 10
# [June 17]
# June 24 \-\- Scott led
# July 1 \-\- Doug led
# [July 8]
# Jul 15 \--Preparation for Methane cruise
# Jul 22 \--Methane cruise
# Jul 29 \--Methane cruise
# [Aug 5]
# [Aug 12]
# [Aug 19]
# [Aug 26]
# [Sep 2]
# [Sep 9] \--CANON cruise, Scholin in England
# [Sep 16]
# Sep 12 \--prep for triple deployment
# [Sep 30]
# [Oct 7]
# Oct 14
# Oct 21
# Oct 28 \--Chris S @ WHOI, Jim at Pices
# [Nov 4]]]></property>
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<property name="body"><![CDATA[Chris found this valve ...
http://www.parker.com/literature/Literature%20Files/Precision%20Fluidics%20Division/UpdatedFiles/PACE%20Data%20Sheet.pdf]]></property>
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<property name="body"><![CDATA[{quote}

{quote}

h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound (33.799, \-118.647).

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deployment-MOE @ M0-\- w/PCR, ISUS.&nbsp; 121 54.11 E; 36 50.10 N.&nbsp; 72m water depth
{color:#33cc00}September 29{color} \-\- Bruce @ offshore (SC) with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; 36 53.75&nbsp; \-122 2.75. 52m water depth.&nbsp; Weight measurements are [HERE|ESPAPP:Weight Calculations for BRUCE|mooring weights].
{color:#33ff00}September 28{color} \-\- Mack @ bight \--&nbsp; no ISUS. no PCR; Using RNALater as preservative.&nbsp; 36 55.95&nbsp; \-121 55.35.&nbsp; 19m water depth.&nbsp; (Lat/Long are from Aaron Gregg after deployment.)

{color:#00cc00}Nov 3{color} \-\- recover all three.  Moe ran out of battery on/around Oct 28.
\\

{color:#ff6666}Nov 30{color} \-\- Deploy D-ESP on MARS.&nbsp; Gordon w/ PCR.&nbsp; Reagents/mission for 2 month deployment.
{quote}
Dec 2 (4pm) lost network connectivity. 48V current went from 3A to 0A; isolation relay triggered, cutting off ethernet.&nbsp; 375V continues powering heater.

Dec 6 \-\- 375V current has dropped to zero.&nbsp; Ball is dead.

Dec 8 \-\- 10:30am, somehow ESPMars rebooted.&nbsp; temp 5.5C when rebooted.
{quote}\\
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<property name="body"><![CDATA[{quote}

{quote}

h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound (33.799, \-118.647).

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deployment-MOE @ M0-\- w/PCR, ISUS.&nbsp; 121 54.11 E; 36 50.10 N.&nbsp; 72m water depth
{color:#33cc00}September 29{color} \-\- Bruce @ offshore (SC) with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; 36 53.75&nbsp; \-122 2.75. 52m water depth.&nbsp; Weight measurements are [HERE|ESPAPP:Weight Calculations for BRUCE|mooring weights].
{color:#33ff00}September 28{color} \-\- Mack @ bight \--&nbsp; no ISUS. no PCR; Using RNALater as preservative.&nbsp; 36 55.95&nbsp; \-121 55.35.&nbsp; 19m water depth.&nbsp; (Lat/Long are from Aaron Gregg after deployment.)

{color:#00cc00}Nov 3{color} \-\- recover all three.  Moe ran out of battery on/around Oct 28.
\\

{color:#ff6666}Nov 30{color} \-\- Deploy D-ESP on MARS.&nbsp; Gordon w/ PCR.&nbsp; Reagents/mission for 2 month deployment.{quote}
Dec 2 (4pm) lost network connectivity. 48V current went from 3A to 0A; isolation relay triggered, cutting off ethernet.&nbsp; 375V continues powering heater.

Dec 6 \-\- 375V current has dropped to zero.&nbsp; Ball is dead.
{quote}\\]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]
# [May 20]
# [May 27]
# June 3
# June 10
# [June 17]
# June 24 \-\- Scott led
# July 1 \-\- Doug led
# [July 8]
# Jul 15 \--Preparation for Methane cruise
# Jul 22 \--Methane cruise
# Jul 29 \--Methane cruise
# [Aug 5]
# [Aug 12]
# [Aug 19]
# [Aug 26]]]></property>
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h2. American Portable Storage

Oakland, CA
1-800-838-4006&nbsp;&nbsp; &nbsp;(Ken)

220V single phase (newer; quiet)
Delivery/pickup $850
$650/mo w/ 2 mo min.&nbsp; Uses $95/mo electricity.

220V 3-phase
$600/mo.&nbsp; Older noisy.&nbsp; Uses $450/mo electricity.



h2. Aztec Containers

Stockton, CA
1-800-399-2126 (Mark)

220 3-phase
Delivery/pickup $495
$695/mo w/ 3 mo min.



h2. Refrigerated Container Services

Oakland, CA
1-510-568-9541

220 3-phase
delivery/pickup \~$500
$1000/mo w/ no minimum.

Could purchase for \~$7800.&nbsp; They may repurchase for ½ price after we're finished.



Reefers only have doors on one end.&nbsp; No lights.&nbsp; Pass-throughs?&nbsp; Unknown.]]></property>
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<property name="body"><![CDATA[\\

h2. American Portable Storage

Oakland, CA
1-800-838-4006&nbsp;&nbsp; &nbsp;(Ken)

220V single phase (newer; quiet)
Delivery/pickup $850
$650/mo w/ 2 mo min.&nbsp; Uses $95/mo electricity.

220V 3-phase
$600/mo.&nbsp; Older noisy.&nbsp; Uses $450/mo electricity.

THIS IS THE COMPANY WE PURCHASED FROM.

Michael McCurley--his quote is [here|^MBARI Quote.doc].

Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].

PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/].


h2. Aztec Containers

Stockton, CA
1-800-399-2126 (Mark)

220 3-phase
Delivery/pickup $495
$695/mo w/ 3 mo min.

h2. Refrigerated Container Services

Oakland, CA
1-510-568-9541

220 3-phase
delivery/pickup \~$500
$1000/mo w/ no minimum.

Could purchase for \~$7800.&nbsp; They may repurchase for ½ price after we're finished.

Reefers only have doors on one end.&nbsp; No lights.&nbsp; Pass-throughs?&nbsp; Unknown.]]></property>
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<property name="body"><![CDATA[\\

h2. American Portable Storage

Oakland, CA
1-800-838-4006&nbsp;&nbsp; &nbsp;(Ken)

220V single phase (newer; quiet)
Delivery/pickup $850
$650/mo w/ 2 mo min.&nbsp; Uses $95/mo electricity.

220V 3-phase
$600/mo.&nbsp; Older noisy.&nbsp; Uses $450/mo electricity.

THIS IS THE COMPANY WE PURCHASED FROM.

Michael McCurley--his quote is [here|^MBARI Quote.doc].

Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].


h2. Aztec Containers

Stockton, CA
1-800-399-2126 (Mark)

220 3-phase
Delivery/pickup $495
$695/mo w/ 3 mo min.

h2. Refrigerated Container Services

Oakland, CA
1-510-568-9541

220 3-phase
delivery/pickup \~$500
$1000/mo w/ no minimum.

Could purchase for \~$7800.&nbsp; They may repurchase for ½ price after we're finished.

Reefers only have doors on one end.&nbsp; No lights.&nbsp; Pass-throughs?&nbsp; Unknown.]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]
# [Feb 16]
# Feb 23 \-\- Oceans Mtg., Portland
# [Mar 2]
# [Mar 9]
# Mar 16 \-\- Jim in S. Cal scouting.  John Ryan ran mtg.
# Mar 23
# Mar 30
# Apr 6 \-\- canceled in preparation for M0 deployment
# Apr 13
# Apr 20
# Apr 27 \--AbSciCon, League City TX
# [May 4]
# [May 11]
# [May 18]
# [Aug 24]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 18 Feb 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [MFB-PCR distribution list] as of 14Jun2010]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris P, Elif, John R., Roman, Allison, Bill, Chris, Jim, Julie


h2. &nbsp;Items Discussed:


h4.


h4. +1.&nbsp; Cold testing+

* Viscometer to arrive late this week
* Standard to arrive today.
* Testing Idea:

# Building of matrix has begun.
# using Wash Buffer with added methanol:

Test Matrix:
|| Temperature || || wash/block alcohol %by v/v \\ || || ||
| room | 0% | 5% | 10% | 15% \\ | 20% \\ |
| 10 | 0% | 5% | 10% | 15% | 20% |
| 4 (or \~2) | 0% | 5% | 10% | 15% | 20% |
* Will look at differences qualitatively, then
* run viscometer, then
* then test on plates, then move to cold instrument.
* &nbsp;
* Chris P. working on SPEdil cold testing.&nbsp; Looks like there are minor changes in pH, depending on precipitation, but unclear if these will have any effect on assay.&nbsp; She will run PCR with calf thymus and various precipitated SPEdil and see if there is any change.

h4. +2.&nbsp; MFB Plans+


* Patty has shipped MFB9 back from Caltech
* Chris P will work on preparing that for Harvard

h4.


h4. +4.&nbsp; Other issues:+

* &nbsp;Will ship McLane pucks back today. Will include some of ours as samples for their machinist.
* Jim will figure out where the next numbering of pucks should begin, for the pucks still to be etched.

Julie presented her results from 2009 field work.

Bill presented his AGU poster. ]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]
# [Feb 16]
# Feb 23 \-\- Oceans Mtg., Portland
# [Mar 2]
# [Mar 9]
# Mar 16 \-\- Jim in S. Cal scouting.  John Ryan ran mtg.
# Mar 23
# Mar 30
# Apr 6 \-\- canceled in preparation for M0 deployment
# Apr 13
# Apr 20
# Apr 27 \--AbSciCon, League City TX
# [May 4]
# [May 11]
# [May 18]
# [Aug 24]
# [Sep 14]
# [Sep 21]
# Sep 28 \-\- Network deployment.&nbsp; no mtg
# Oct 5
# Oct 12
# Oct 19
# Oct 26 \-\- Chris S. @ WHOI, Jim at PICES
# [Nov 2]
# [Nov 9]
# [Nov 30]  \--Year re-cap]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound (33.799, \-118.647).

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deployment-MOE @ M0-\- w/PCR, ISUS.&nbsp; 121 54.11 E; 36 50.10 N.&nbsp; 72m water depth
{color:#33cc00}September 29{color} \-\- Bruce @ offshore (SC) with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; 36 53.75&nbsp; \-122 2.75. 52m water depth.&nbsp; Weight measurements are [HERE|ESPAPP:Weight Calculations for BRUCE|mooring weights].
{color:#33ff00}September 28{color} \-\- Mack @ bight \--&nbsp; no ISUS. no PCR; Using RNALater as preservative.&nbsp; 36 55.95&nbsp; \-121 55.35.&nbsp; 19m water depth.&nbsp; (Lat/Long are from Aaron Gregg after deployment.)

{color:#00cc00}Nov 3{color} \-\- recover all three.  Moe ran out of battery on/around Oct 28.\\

{color:#ff6666}Nov 30{color} \-\- Deploy D-ESP on MARS.&nbsp; Gordon w/ PCR.&nbsp; Reagents/mission for 2 month deployment.Dec 2 (4pm) lost network connectivity.&nbsp; 48V current went from 3A to 0A; isolation relay triggered, cutting off ethernet.&nbsp; 375V continues powering heater.

Dec 6 \-\- 375V current has dropped to zero.&nbsp; Ball is dead. ]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound (33.799, \-118.647).

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deployment-MOE @ M0-\- w/PCR, ISUS.&nbsp; 121 54.11 E; 36 50.10 N.&nbsp; 72m water depth
{color:#33cc00}September 29{color} \-\- Bruce @ offshore (SC) with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; 36 53.75&nbsp; \-122 2.75. 52m water depth.&nbsp; Weight measurements are [HERE|ESPAPP:Weight Calculations for BRUCE|mooring weights].
{color:#33ff00}September 28{color} \-\- Mack @ bight \--&nbsp; no ISUS. no PCR; Using RNALater as preservative.&nbsp; 36 55.95&nbsp; \-121 55.35.&nbsp; 19m water depth.&nbsp; (Lat/Long are from Aaron Gregg after deployment.)

{color:#00cc00}Nov 3{color} \-\- recover all three.  Moe ran out of battery on/around Oct 28.]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound.

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0 ]]></property>
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<property name="body"><![CDATA[This is the documentation to detail out the design of the state representation interface between the GUI application and the instrument itself.  This interface will allow the GUI (and other applications) to get information about the current state of the various components of the ESP.

Some details about the interface:

# The ESP application (server) shall listen on a fixed TCP socket.
# Any number clients can connect to this socket, each thereby opening a separate, private, bidirectional, ASCII connection to the ESP server.
# The server will respond to the following client commands:
##  List all available states
### Each state is identified by a short ASCII(symbolic) name. Metadata shall include:
#### Description  e.g.  Storage carousel
#### sprintf format string  e.g.  %.2fml
#### range  (min and max expected values)
#### hardware failures may cause reported values to be out of range
## Subscribe to updates on (only) the specified states
{note}
This limits subsequent state updates to just those listed by their symbolic names. This message is required because it determines the ordering of states in vectors described below.
{note}
## Refresh all subscribed states
{note} 
All the subscribed states are sent to the client in the order in which they were listed in the most recent subscribe message.
{noformat}
<timestamp?  seconds since epoch??>
<new value[0]>
<new value[1]>
...
<new value[n-1]>
{noformat}
## where n is the number of states subscribed.  This establishes a baseline from which subsequent state changes are reported.
{note}
##  Request C more changed state updates at maximum rate one per t tenths of seconds.

   The client tells the server it is ready to receive C more state change responses
   and that the server may emit these at a rate no faster than one every t tenths of a second.

   A client wishing to continuously monitor state should send a new request
   shortly *before*  the last update (as allowed by the previous request) has been received.
   If C is kept small (say 10 or so), this mechanism will ensure that update
   messages don't back up on the networking queue, while avoiding paying
   any network latency penalty.  (Similar to TCP's sliding window mechanism)

   The client can stop updates by requesting 0 more at some arbitrary rate.

   Only those states whose values changed since the last update will be sent
   Format will be a list of elements, each of the form:
<index>,<new value>
   where:
       index = an integer from 0 to n-1 where n is the number of subscribed states
       new value = number conforming to the state's sprintf format string
    note that the unit suffix will be omitted.  (i.e. 0.2 not 0.2ml)


Notes:
  Mostly to myself :-)

  Normally, all I2C messages between the Linux host and the dwarves are logged.
  However, this protocol will require continuous polling of all the subscribed dwarves'
  raw positions.  Nothing else currently does anything like this (by design! :-)
  Clearly, such messages should not be logged.  Further, it may be necessary to
  add an I2C message to the dwarf firmware that queries raw position only.  The existing
  full status poll message returns lots of extraneous engineering info like velocity,
  electrical current, etc.]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
## Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
## Or you should be able to double click on the jar in most cases.
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


]]></property>
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<property name="body"><![CDATA[For several aspects of the ESP GUI application, the application will have to have an associated user, which will, in turn, belongs to specifics groups.  The reason for this is that we do not want the application to allow any user to do all things in the ESP GUI.  For example:

# Maybe you want to limit users to read-only.
# Certain users can create mission scripts for certain ESP instrument
# Certain users can delete deployment information.
# etc.

In order to enable this type of access control, the Java SE security infrastructure was utilized in the GUI development.

Resources:

# [http://download.oracle.com/javase/7/docs/technotes/guides/security/overview/jsoverview.html|Java SE Security Overview]]]></property>
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<property name="body"><![CDATA[For several aspects of the ESP GUI application, the application will have to have an associated user, which will, in turn, belongs to specifics groups.  The reason for this is that we do not want the application to allow any user to do all things in the ESP GUI.  For example:

# Maybe you want to limit users to read-only.
# Certain users can create mission scripts for certain ESP instrument
# Certain users can delete deployment information.
# etc.

In order to enable this type of access control, the Java SE security infrastructure was utilized in the GUI development.

Resources:

# [Java SE Security Overview|http://download.oracle.com/javase/7/docs/technotes/guides/security/overview/jsoverview.html]]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]
# [May 20]
# [May 27]
# June 3
# June 10
# [June 17]
# June 24 \-\- Scott led
# July 1 \-\- Doug led
# [July 8]
# Jul 15 \--Preparation for Methane cruise
# Jul 22 \--Methane cruise
# Jul 29 \--Methane cruise
# [Aug 5]
# [Aug 12]
# [Aug 19]
# [Aug 26]
# [Sep 2]
# [Sep 9] \--CANON cruise, Scholin in England]]></property>
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<property name="body"><![CDATA[This is the documentation to detail out the design of the state representation interface between the GUI application and the instrument itself.  This interface will allow the GUI (and other applications) to get information about the current state of the various components of the ESP.

Some details about the interface:

# The ESP application (server) shall listen on a fixed TCP socket.
# Any number clients can connect to this socket, each thereby opening a separate, private, bidirectional, ASCII connection to the ESP server.
# The server will respond to the following client commands:
##  List all available states
### Each state is identified by a short ASCII(symbolic) name. Metadata shall include:
#### Description  e.g.  Storage carousel
#### sprintf format string  e.g.  %.2fml
#### range  (min and max expected values)
#### hardware failures may cause reported values to be out of range
## Subscribe to updates on (only) the specified states
{note}
This limits subsequent state updates to just those listed by their symbolic names. This message is required because it determines the ordering of states in vectors described below.
{note}
## Refresh all subscribed states
{note} 
All the subscribed states are sent to the client in the order in which they were listed in the most recent subscribe message.
{noformat}
<timestamp?  seconds since epoch??>
<new value[0]>
<new value[1]>
...
<new value[n-1]>
{noformat}
where n is the number of states subscribed.  This establishes a baseline from which subsequent state changes are reported.
{note}
## Request C more changed state updates at maximum rate one per t tenths of seconds.
{note}
* The client tells the server it is ready to receive C more state change responses and that the server may emit these at a rate no faster than one every t tenths of a second.
* A client wishing to continuously monitor state should send a new request shortly *before*  the last update (as allowed by the previous request) has been received. If C is kept small (say 10 or so), this mechanism will ensure that update messages don't back up on the networking queue, while avoiding paying any network latency penalty.  (Similar to TCP's sliding window mechanism)
* The client can stop updates by requesting 0 more at some arbitrary rate.
* Only those states whose values changed since the last update will be sent
* Format will be a list of elements, each of the form:
{noformat}
<index>,<new value>
{noformat}
where:
* index = an integer from 0 to n-1 where n is the number of subscribed states
* new value = number conforming to the state's sprintf format string (note that the unit suffix will be omitted, i.e. 0.2 not 0.2ml)
{note}

# Notes (Mostly for Brent :-))
{note}
Normally, all I2C messages between the Linux host and the dwarves are logged. However, this protocol will require continuous polling of all the subscribed dwarves' raw positions.  Nothing else currently does anything like this (by design! :-). Clearly, such messages should not be logged.  Further, it may be necessary to add an I2C message to the dwarf firmware that queries raw position only.  The existing full status poll message returns lots of extraneous engineering info like velocity, electrical current, etc.
{note}]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Doug, Wayne, Scott, Cheri
Absent:&nbsp;&nbsp; Chris S., Addie (maternity)

h3. Machine Builds


h3. MFB


h3. Software

* &nbsp;y

h3. DWSM


h6. +Sphere+

* &nbsp;Mack.
\\

h6. +Elevator+

* &nbsp;ce the D-ESP.

*{+}DWSM{+}*
* arves.

h3. Other Items:

* &nbsp;C.]]></property>
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<id name="id">9404425</id>
<property name="body"><![CDATA[Short, touch-base meeting with Jim, Scott, Brent, Kevin, Wayne.]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">9404420</id>
<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|ESP Automated Image Analysis]

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter 
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size. 
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. Automated Image Analysis.

Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found [here|ESP Automated Image Analysis]

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter 
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size. 
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Doug, Wayne, Scott, Cheri
Absent:&nbsp;&nbsp; Chris S., Addie (maternity)

h3. Machine Builds


h3. MFB


h3. Software

* &nbsp;y

h3. DWSM


h6. +Sphere+

* &nbsp;Mack.
\\

h6. +Elevator+

* &nbsp;ce the D-ESP.

*{+}DWSM{+}*
* arves.

h3. Other Items:

* &nbsp;C.]]></property>
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<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+

June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.

June 24 \-\- Sea van leaves NZ.  Scheduled to arrive Oakland July 15.

h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.
\\

h3. {color:#ff00ff}NOAA/Woods Hole Deployment of ESPFRIDAY{color}

May 16-17 \-\- Scouting trip to Friday Harbor for shed build and comms checking

June 2 \-\- ESP Friday deployed on dock.  Tentative to end July 16.
]]></property>
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<property name="body"><![CDATA[{quote}

{quote}

h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound (33.799, \-118.647).

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deployment-MOE @ M0-\- w/PCR, ISUS.&nbsp; 121 54.11 E; 36 50.10 N.&nbsp; 72m water depth
{color:#33cc00}September 29{color} \-\- Bruce @ offshore (SC) with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; 36 53.75&nbsp; \-122 2.75. 52m water depth.&nbsp; Weight measurements are [HERE|ESPAPP:Weight Calculations for BRUCE|mooring weights].
{color:#33ff00}September 28{color} \-\- Mack @ bight \--&nbsp; no ISUS. no PCR; Using RNALater as preservative.&nbsp; 36 55.95&nbsp; \-121 55.35.&nbsp; 19m water depth.&nbsp; (Lat/Long are from Aaron Gregg after deployment.)

{color:#00cc00}Nov 3{color} \-\- recover all three.  Moe ran out of battery on/around Oct 28.
\\

{color:#ff6666}Nov 30{color} \-\- Deploy D-ESP on MARS.&nbsp; Gordon w/ PCR.&nbsp; Reagents/mission for 2 month deployment.

{quote}
Dec 2 (4pm) lost network connectivity. 48V current went from 3A to 0A; isolation relay triggered, cutting off ethernet.&nbsp; 375V continues powering heater.

Dec 6 \-\- 375V current has dropped to zero.&nbsp; Ball is dead.

Dec 8 \-\- 10:30am, somehow ESPMars rebooted.&nbsp; temp 5.5C when rebooted.

Dec 9 \-\- 2:30pm.&nbsp; Restarted mission.
{quote}\\
\\
\\]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010]]></property>
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<id name="id">15663349</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [MFB-PCR distribution list] as of 14Jun2010]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Doug, Wayne, Cheri, Chris S.
Absent:&nbsp;&nbsp; Scott, Addie (maternity)

h3. Machine Builds


h3. MFB


h3. Software

* &nbsp;y

h3. DWSM


h6. +Sphere+

* &nbsp;Still in parking deck.&nbsp; Will be moved to tin-shed by facilities people.
* &nbsp;Doug to look into purchase of a (folding?) engine hoist for moving stuff within the van.
* Doug has designed center spider hanger cage for holding ESP core within the sphere.&nbsp; Parts to get to the shop today.

h6. +Elevator+

* &nbsp;We've decided the modem to purchase (w/ deckbox).&nbsp; Will cost $27K.&nbsp; Will charge to 900915.99.&nbsp; 10-week lead time, although this isn't needed until June.

*{+}DWSM{+}*
* Bad pump has been sent back and will be repaired/replaced.

h3. Other Items:

* &nbsp;Refrigerated van has been ordered and will arrive next Tues/Weds (Feb 24/25).&nbsp; Call had gone in to Greg Voogd about setting up electrical hook-up.&nbsp; We will wait for Danny Day to do wiring, using extension cords if necessary for lighting.&nbsp; Once van here, we'll convene on where wiring/lights should be installed.]]></property>
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<id name="id">15663356</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# 2011 Deployments
# [MFB-PCR distribution list] as of 4Nov2010]]></property>
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<property name="body"><![CDATA[# Science Meetings
# Engineering Meetings
# Software Development Meetings]]></property>
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<property name="body"><![CDATA[h2. Engineering meeting


h4. &nbsp;Items:

* &nbsp;In 2011, we may swap a Zephyr day (May 19) to later and use Shana Rae on the 19th.
* Much discussion about the ship schedule in 2011.

Teledyne may become more involved in the engineering process with G3.&nbsp; We will get an NDA and MOU in&nbsp; place and possible host them at a mid/late Jan/Feb meeting.&nbsp; Chris going to visit them and see if they are interested in participating.
\\

h5. +G3+

* &nbsp;A system level diagram showing concepts needed.
* We should start from G2; e.g., 40 samples over 3 weeks would be a good minimum
* what about looking at sampling workshop output for sampling requirements?&nbsp; Chris S. will look to John R. to get this together.&nbsp; See what potential users want to do.

h5. +MARS+

&nbsp;We may move the recovery day from Jan 31to later in that week.

Adaptive SamplingWe will run the algorithm on shore and then push the 'decision' to the instrument.&nbsp; Brent to work on it this deployment.

Maybe use temperature as signal ;&nbsp; 3 runs when temp drops, 3 when temp rises, 3 when mid temp.&nbsp; Should stay simple if code is not ready

We need to retain 8 samples in reserve for this.&nbsp; Terminate mission the end of the first week of Jan.
Must push a patch down to DWSM as we think a compliance&nbsp; bag is broken.

h5. +&nbsp;G2+

Super-Clamp is only on Gordon right now.&nbsp; We have coaxial alignment pieces, but still need springs.&nbsp; Doug to order. ]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]
# [May 20]
# [May 27]
# June 3
# June 10
# [June 17]
# June 24 \-\- Scott led
# July 1 \-\- Doug led
# [July 8]
# Jul 15 \--Preparation for Methane cruise
# Jul 22 \--Methane cruise
# Jul 29 \--Methane cruise
# [Aug 5]
# [Aug 12]
# [Aug 19]
# [Aug 26]
# [Sep 2]
# [Sep 9] \--CANON cruise, Scholin in England
# [Sep 16]
# Sep 12 \--prep for triple deployment
# [Sep 30]
# [Oct 7]
# Oct 14
# Oct 21
# Oct 28 \--Chris S @ WHOI, Jim at Pices
# [Nov 4]
# [Dec 9]]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...]]></property>
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<property name="body"><![CDATA[h4.


h4. {color:#ff00cc}SCRIPPS-Lab Run \-\- ESP-Waldo{color}

*&nbsp;April 27, 2015*

Roman delivers ESP Waldo to Andy Allen's lab at CVGI.&nbsp; Idea was to collect archived sample twice/week for \~6 months to test longevity issues with filters.

mid-June, instrument started losing comms to elevator dwarf.&nbsp; Roman sent down to replace dwarf on June 29-30. Re-canned and restarted mission.

RECOVERY

Roman recovers ESP-Waldo October 6, 2015.

h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce. Divers: Kim R., Paul C.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

Divers: Paul C., Jeff Sevadjian

{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload. Divers: Eric R, Jeff Sevadjian
\\

h4. {color:#ff00cc}1st MAKAI flight w 5 cartridges{color}

*July 22, 2015*

Flew triangle pattern after launch.&nbsp; Makai found chlorophyll feature, and we fired two cartridges while flying through.&nbsp; First cartridge may have had sticky valve and stayed in by-pass (filtered 1L in \~20 minutes; too fast).&nbsp; Second cartridge seemed to have worked.

Some issues with ESP not communicating it was on, and then LRAUV not turning it on.&nbsp; Went to recover vehicle late July 23, but did not surface until mission timed-out, after we were already ashore.&nbsp; That was when we discovered the comms issues.&nbsp; Fixed one, tried to fire during a 'night operation' Thursday evening.&nbsp; Discovered Friday morning a second comms issues, which was fixed, and fired the 3 samples during day on Friday, July 24.&nbsp; Did keep-station all weekend, and recovered LRAUV early Monday morning (July 27).

Results:

1.&nbsp; Cartridge #1 bypassed 1L (toroid valve stuck; sea water ran through instrument in bypass mode; 7 minutes); flying through feature (chl=3.0 ug/l; 10.97m)

2. &nbsp; #2 filtered 815.8ml; flying through feature (11.03m; chl=3.3 ug/l; took 53 minutes)

3. &nbsp; #3 filtered 802.3ml;&nbsp; within feature (13.8m; chl=3.02 ug/l; took 51 minutes)

4. &nbsp; #4 filtered 759.6ml,&nbsp; above feature (7.1m; chl=1.11 ug/l; took 50 minutes)

5.&nbsp;&nbsp; #5 filtered 809.1ml,&nbsp; below feature (19.4m; chl=4.24 ug/l; took 51 minutes)

Excellent summary paper by Yanwu Zhang about what the LRAUV did during this deployment-\-[here|^Zhang_etal_chlpeak.pdf|Yanwu's paper].(check your download folder)

h4. {color:#ff00cc}SCRIPPS-Del Mar Mooring \-\- ESP-Waldo{color}

*&nbsp;November 12, 2015*

Roman and Scott drive down Nov 8 and work for the week to assemble mooring.&nbsp; Goes in water on the 12th (check ESP-Waldo channel on Slack for pictures).&nbsp; Setup has SCRIPPS modem as master mooring controller.&nbsp; when it sends command string to ESP, ESP and ESP-modem awake, which allows us to get into ESP for diagnosis and large data transfers.&nbsp; At end of sampling, ESP and it's modem goes to sleep.&nbsp; Currently (Dec 1) using [this|^ESP deploy _DelMar_sampling_127.xlsx|Sampling schedule as of Dec 1] sampling schedule.

Dec 6, 2015

I2C error has stopped our sampling mission.&nbsp; ESP now providing only CTD updates.&nbsp; Brent's message:&nbsp; "The problem that surfaced first last Wednesday has recurred and is not going away this time.

Waldo's ESP host can access the sleepy microcontroller to get can status, etc., however, sleepy cannot access anything on the I2C bus."

Dec 14, 2015

I2C bus was back online\!&nbsp; Instrument had been left 'on' since last communications, and had some rough weather over this weekend.&nbsp; Brent was able to get in and unstick the hand then take a 'flawless' sample.&nbsp; Will see how she works in four days...
\\

h4. {color:#ff00cc}MAKAI flight w 4 Archives, 1 Lyse-n-go{color}

*Dec 18-21, 2015*

Launch/recover from MLML rib boat.&nbsp; Multiple failures with LRAUV; difficulty holding (shallow) depth, thruster errors. Original idea was to find a chl feature, take 2 archives.&nbsp; Dive below feature, take two archives.&nbsp; Reacquire feature, fire off l-n-g.&nbsp; With multiple vehicle errors and time running out (Holiday break; people leaving) we got one shallow archive, one deep, and ran the l-n-g deep.&nbsp; No feature ever found--very stormy and little stratification. Brett, Brian, Chris P on deployment; Brett, Ben, Jim on recovery.]]></property>
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<property name="body"><![CDATA[{quote}

{quote}

h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound (33.799, \-118.647).

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deployment-MOE @ M0-\- w/PCR, ISUS.&nbsp; 121 54.11 E; 36 50.10 N.&nbsp; 72m water depth
{color:#33cc00}September 29{color} \-\- Bruce @ offshore (SC) with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; 36 53.75&nbsp; \-122 2.75. 52m water depth.&nbsp; Weight measurements are [HERE|ESPAPP:Weight Calculations for BRUCE|mooring weights].
{color:#33ff00}September 28{color} \-\- Mack @ bight \--&nbsp; no ISUS. no PCR; Using RNALater as preservative.&nbsp; 36 55.95&nbsp; \-121 55.35.&nbsp; 19m water depth.&nbsp; (Lat/Long are from Aaron Gregg after deployment.)

{color:#00cc00}Nov 3{color} \-\- recover all three.  Moe ran out of battery on/around Oct 28.
\\

{color:#ff6666}Nov 30{color} \-\- Deploy D-ESP on MARS.&nbsp; Gordon w/ PCR.&nbsp; Reagents/mission for 2 month deployment.\\
{quote}
Dec 2 (4pm) lost network connectivity. 48V current went from 3A to 0A; isolation relay triggered, cutting off ethernet.&nbsp; 375V continues powering heater.

Dec 6 \-\- 375V current has dropped to zero.&nbsp; Ball is dead.

Dec 8 \-\- 10:30am, somehow ESPMars rebooted.&nbsp; temp 5.5C when rebooted.

Dec 9 \-\- 2:30pm.&nbsp; Restarted mission.\\

Dec 23 \-\- lost communications soon after 6:20pm.&nbsp; 375V stopped drawing on Dec 28.
{quote}\\
\\
\\
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)
\\ \\]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began?? and ended ~ week later when pump tore from piling.


*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).
Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays
Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

MELO used was #300034012090780

location reported by MELO was-\- &nbsp; 33.4865 \-118.51285

*March 20*\--lost comms

*March 21*\--re-established comms and think problem in E/M cable.

*March 22*\--lost comms

*April 3*\--small boat to buoy to test E/M cable

*April 8*\--'rescue' mission. Swapped E/M cables and repositioned in slightly deeper water, at 33.48504 \-118.50988

*May 1*\--mission ended and mooring recovered.

h4. {color:#ff00cc}ECOHAB--S. California{color}

*April 1*\--Instruments deployed

&nbsp;MOE--inshore at 33.60779 \-118.01877 with ISUS

Melo was 300234060014550

avg can depth \~9m
\\

&nbsp;Bruce--offshore at 33.58609 \-118.03686

Melo was 300234060016190

avg can depth \~19.5m

*~ April 9* lost communication with Bruce.&nbsp;

*April 15*\--Rescue mission w/Nerissa found 'hung' modem.&nbsp; Power cycled and checked cables on deck.&nbsp; Re-deployed in nearby spot.&nbsp; Divers (Kim R. & George M) measured 17.7m to top of can, 25.3 m to master link.

*May 2*\--Mission ended and recovered both instruments ]]></property>
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<property name="body"><![CDATA[{quote}

{quote}

h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound (33.799, \-118.647).

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deployment-MOE @ M0-\- w/PCR, ISUS.&nbsp; 121 54.11 E; 36 50.10 N.&nbsp; 72m water depth
{color:#33cc00}September 29{color} \-\- Bruce @ offshore (SC) with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; 36 53.75&nbsp; \-122 2.75. 52m water depth.&nbsp; Weight measurements are [HERE|ESPAPP:Weight Calculations for BRUCE|mooring weights].
{color:#33ff00}September 28{color} \-\- Mack @ bight \--&nbsp; no ISUS. no PCR; Using RNALater as preservative.&nbsp; 36 55.95&nbsp; \-121 55.35.&nbsp; 19m water depth.&nbsp; (Lat/Long are from Aaron Gregg after deployment.)

{color:#00cc00}Nov 3{color} \-\- recover all three.  Moe ran out of battery on/around Oct 28.
\\

{color:#ff6666}Nov 30{color} \-\- Deploy D-ESP on MARS.&nbsp; Gordon w/ PCR.&nbsp; Reagents/mission for 2 month deployment.
\\
{quote}

{quote}Dec 2 (4pm) lost network connectivity. 48V current went from 3A to 0A; isolation relay triggered, cutting off ethernet.&nbsp; 375V continues powering heater.

Dec 6 \-\- 375V current has dropped to zero.&nbsp; Ball is dead.

Dec 8 \-\- 10:30am, somehow ESPMars rebooted.&nbsp; temp 5.5C when rebooted.

Dec 9 \-\- 2:30pm.&nbsp; Restarted mission.
\\

Dec 23 \-\- lost communications soon after 6:20pm.&nbsp; 375V stopped drawing on Dec 28.
{color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS
\\
\\
\\
\\]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began

*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).
Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays
Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

MELO used was #300034012090780

location reported by MELO was-\- &nbsp; 33.4865 \-118.51285

*March 20*\--lost comms

*March 21*\--re-established comms and think problem in E/M cable.

*March 22*\--lost comms

*April 3*\--small boat to buoy to test E/M cable

*April 8*\--'rescue' mission. Swapped E/M cables and repositioned in slightly deeper water, at 33.48504 \-118.50988

*May 1*\--mission ended and mooring recovered.


h4. {color:#ff00cc}ECOHAB--S. California{color}

*April 1*\--Instruments deployed

&nbsp;MOE--inshore at 33.60779 \-118.01877 with ISUS

Melo was 300234060014550

avg can depth \~9m
\\

&nbsp;Bruce--offshore at 33.58609 \-118.03686

Melo was 300234060016190

avg can depth \~19.5m

*~ April 9* lost communication with Bruce.&nbsp;

*April 15*\--Rescue mission w/Nerissa found 'hung' modem.&nbsp; Power cycled and checked cables on deck.&nbsp; Re-deployed in nearby spot.&nbsp; Divers (Kim R. & George M) measured 17.7m to top of can, 25.3 m to master link.

*May 2*\--Mission ended and recovered both instruments ]]></property>
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<property name="body"><![CDATA[{quote}

{quote}

h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound (33.799, \-118.647).

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR

{color:#0000ff}August 30{color}; Recover NEO from M0

{color:#996600}September 14{color} \-\- deploy drifter (Mack, no PCR) off Western Flyer
{color:#996600}September 19{color} \-\- recover drifter
\\

{color:#33ff00}September 28{color} \-\- Triple deployment-MOE @ M0-\- w/PCR, ISUS.&nbsp; 121 54.11 E; 36 50.10 N.&nbsp; 72m water depth
{color:#33cc00}September 29{color} \-\- Bruce @ offshore (SC) with LISST, no PCR, no ISUS.&nbsp; Using saline EtOH as preservative.&nbsp; 36 53.75&nbsp; \-122 2.75. 52m water depth.&nbsp; Weight measurements are [HERE|ESPAPP:Weight Calculations for BRUCE|mooring weights].
{color:#33ff00}September 28{color} \-\- Mack @ bight \--&nbsp; no ISUS. no PCR; Using RNALater as preservative.&nbsp; 36 55.95&nbsp; \-121 55.35.&nbsp; 19m water depth.&nbsp; (Lat/Long are from Aaron Gregg after deployment.)

{color:#00cc00}Nov 3{color} \-\- recover all three.  Moe ran out of battery on/around Oct 28.
\\

{color:#ff6666}Nov 30{color} \-\- Deploy D-ESP on MARS.&nbsp; Gordon w/ PCR.&nbsp; Reagents/mission for 2 month deployment.
\\
{quote}

{quote}
Dec 2 (4pm) lost network connectivity. 48V current went from 3A to 0A; isolation relay triggered, cutting off ethernet.&nbsp; 375V continues powering heater.

Dec 6 \-\- 375V current has dropped to zero.&nbsp; Ball is dead.

Dec 8 \-\- 10:30am, somehow ESPMars rebooted.&nbsp; temp 5.5C when rebooted.

Dec 9 \-\- 2:30pm.&nbsp; Restarted mission.
\\

Dec 23 \-\- lost communications soon after 6:20pm.&nbsp; 375V stopped drawing on Dec 28.

{color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS
\\
\\
\\
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<property name="body"><![CDATA[Makai Flight

Feb 3-5, 2016

&nbsp;Flew 1 ]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}MAKAI flight w 4 Archives, 1 Lyse-n-go{color}

*Feb 2-4, 2015*

Repeat of Dec flight.&nbsp; Here are notes from Yanwu's summary:

(Note: when reaching each target depth (peak-chl or pre-set), we give Makai 10 minutes to damp down depth undulation.)

Sample#1 (lyse&go sample. At chl peak):
Makai descended from surface, found the chl peak at 8.7m. On the ensuing ascent, Makai held depth at 8.7m, and triggered sample#1.
Took 63 minutes to complete.&nbsp; Then Makai surfaced to "report to shore".

Sample#2 (archive sample. At chl peak):
Makai descended from surface, found the chl peak at 12.7m. On the ensuing ascent, Makai held depth at 12.3m, and triggered sample#2. (Note: the water column was quite mixed vertically. The chl values at 8m and 12m were very close. Makai was doing her best to pick the relatively weak peak.)&nbsp; Took 41 minutes to complete.

Sample#3 (archive sample. At reacquired chl peak):
In order to reacquire the chl peak (considering the peak-chl layer may have moved up or down), Makai intentionally wiggled up and down (up first, then down, and then up). On the "down", it found the chl peak at 13.2m. On the ensuing "up", Makai held depth at 13.0m, and triggered sample#3.&nbsp; Took 40 minutes to complete.

Sample#4 (archive sample. At pre-set 27m. Control sample.):
Makai dove to the pre-set 27m depth, and triggered sample#4.&nbsp; Took 39 minutes to complete.

Sample#5 (archive sample. At pre-set 27m. Control sample.):
Makai stayed at the pre-set 27m depth, and triggered sample#5.&nbsp; Took 38 minutes to complete. ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Doug, Wayne, Cheri, Chris S., Scott, Gene
Absent:&nbsp; Addie (maternity)

h3. Machine Builds

* &nbsp;Gordon and Betty
** hand builds;&nbsp; modifications are in the shop but not an official shop work order
** some parts simply made incorrectly (El Camiino)
** Cheri will put into system today and we will prioritize
* Shallow lids
** simply use different port on lid so no modification needed.
** will use old power hole for Gene's pressure transducer
** Bottom line:&nbsp; No new hole in lids.&nbsp; Doug looking into whether there is a seal available.
* Light Puck
** The Phase config file was to be machine independent.&nbsp; But now we're seeing differences in cameras, so Brent's putting a machine-specific 'multiplier' into the phase config that references each individual camera.
** In the light puck vs. matched-array comparison, results are difficult to interpret.&nbsp; Will be using matched-array results so we will have instrument-specific calibrations--not ideal.&nbsp; For the moment, every machine has its own calibration & we'll multiply to make them the 'same'.&nbsp; Eventually the calibration will be empirically derived.
* Bruce is out of focus.&nbsp; Will not touch until after April 1 deployment.

h3. MFB

* MFB's to ship to McLane this PM.&nbsp; Will ship without PCR tubing.

h3. Drifter

* Design review today at 1:30 to discuss issues that may impact the foam design
* 1st test deployment is May 14.
* Must mount in ESP can:&nbsp; pressure transducer, accelerometer, serial->ethernet, ethernet hub and extender.&nbsp; Gene to work with Scott and Doug on this.
* Top-side
** Cable goes to slip-ring \--> eventually to host board that'll talk to Iridium modem.&nbsp; Host boards on top will need DHCP--otherwise we need to assign static IP addresses
** Gene has found that modems are soon to be obsolete--Dec 2009.&nbsp; $1750 ea/ we need 2.&nbsp;&nbsp; Gene looking into buying new vs. old.&nbsp; We could simply borrow one for test deployments.
** Brent wants to get old phone modems to do testing that will exercise our software.
** Plan is to use lead-acid batteries in plastic pipe.&nbsp; This setup is putting off the ultimate alkaline battery pack build.
** NEXT meeting will update on fitting stuff into core.\\

h3. Software

* &nbsp;dPress code ready for testing.&nbsp; Wayne will load Monday AM
* Brent not started on DWSM yet.

h3. Deep ESP

* ISUS
** Luk says they have a 4km housing; just need a new probe--a PO away.&nbsp;
** We WILL NOT put ISUS on elevator in June
** John Ryan is taking over ISUS work.&nbsp; We may eventually want a TI housing.&nbsp; Craig Okuda may havve one for us (or a design)

h6. +Sphere+

* Spider construction.&nbsp; All parts are machine shop.&nbsp; Will be finished today.
* Frank F. will do welding week after next in the high-bay.&nbsp; We'll have to get the sphere bottom out of its crate for that.

h6. +Elevator+

* Foam should be ready March 15.
* Frame has been shipped to LA for heat treating.
* doug has ordered shock-load feet.

*{+}DWSM{+}*
* spider being welded today.&nbsp; sphere bottom is in machine shop.
* Power budget for modems not figured yet.&nbsp; this is critical path for June deployments, not earlier.
* interface boards ready next week.
* Big issue is high pressure pump:
** 2 pumps are bad:&nbsp; 1st is being repaired--stuck piston, 2nd showing same issues.&nbsp; Either too much air in it or debris.&nbsp; Doug waiting to hear from manufacturer on why they aren't working and he has some ideas for modifying pump.
** 1 bad motor--melted plastic inside, but then broke free; it now 'works', but is not trustworthy enough to deploy.
* Much discussion on whether we should have a timed or thermal time-out in software to shut pump down.&nbsp; {color:#cc0000}I was unclear what was decided.{color}

h3. Other Items:

* &nbsp;Van:&nbsp; Doug has provided sketch of outlets (16) and lights to Greg Voogd
** we will push ESP to front of van and build a false wall so only front needs cooling
** I
** Need to check with Chris Grech about powering the van on UNOLS ships--what do we need?
** Greg will level the van next week.
** W
* &nbsp;]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [The MFB User's Manual]
# [MFB command help sheet|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1_7%2010_03_2008.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/Fluidics_worksheet_04Dec08.pdf]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]]]></property>
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<property name="body"><![CDATA[Here is the information for the data model that was created to back the information needed in the GUI.
!core model.jpg|align=centre!]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes (no longer maintained--Sep 2012)


# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
# [2014 Deployments]
# [2015 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h4. (as of Mar 28, 2013)


h3. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m (bare)*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

*21.5m*

Now (Apr 2014) with bad connector...
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos [here|^Image 3.jpg|corrosion] and [here|^Image 2.jpg|salt crystals].

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)

*15.2m*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h3. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]]]></property>
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<property name="body"><![CDATA[h4. (as of Mar 28, 2013)


h3. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 day S. Cal ECOHAB w/ Bruce (Mar 2013)
* xx days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m (bare)*

*25.3m*

* Catalina Island replacement (April 2014).&nbsp; Installed April 8.

*21.5m*

Now (Apr 2014) with bad connector...

* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos [here|^Image 3.jpg|corrosion] and [here|^Image 2.jpg|salt crystals].

*15.6m*

* 35 day S. Cal ECOHAB w/Mack (Mar 2013)
* 41 day MB ECOHAB w/Mack (Sep 2013)
* 30 day S. Cal ECOHAB w/Mack (Apr 2014)

*15.2m*

* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h3. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Other
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

h3. Parsing Rules

A normal flow of a log file might then look like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Events
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
# Mission End
{noformat}
.mGoodNews.email "moe completed 09nov03moe mission",:Subject=>"Ready to Recover"
{noformat}

In graphical form, the flow of a ESP log might look something like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop

h3. Parsing Rules

A normal flow of a log file might then look like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

h3. Important log entries

h5. Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}

h5. Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}

h5. Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}

h5. HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}

h5. PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}

h5. PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}

h5. Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}

h5. Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}

h5. Other

{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop


h3. Important log entries

Using the above information, I went through several log files and extracted entries that correspond to important things in the GUI application:

# Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}
## Ancillary Data Entry
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}
## Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}
### Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}
## HABDA with WCR starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
{noformat}
## PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}
### PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}
### Image acquisition during PCR
{noformat}
#"sh2"Imaging sh2 puck in Processing Clamp while storing it to tube 2
#"sh2"Lights, camera, ACTION!
#"sh2"\PuckCamera: snap -bin=1,1 160.0 /var/log/esp/hires/pcr09sep3008h575ml160s.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/pcr09sep3008h575ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40.0 /var/log/esp/pcr09sep3008h575ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/pcr09sep3008h575ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/pcr09sep3008h575ml.tif
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 79.518 seconds\
/var/log/esp/midres/pcr09sep3008h575ml.tif: TIFF Upload Complete\

."Qmail"BACfans.email "79.518 sec auto-exposure",:Subject=>"pcr09sep3008h575ml images!"
{noformat}
## Other
{noformat}
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"
#"brent 7096"\Session Begun
{noformat}

h3. Parsing Rules

A normal flow of a log file might then look like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:

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<id name="id">11829319</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop

h3. Parsing Rules

A normal flow of a log file might then look like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}

h3. Important log entries

h5. Mission start

h5. Whole Cell Archive running:
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}

h5. PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}

h5. Other

{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"

."Qmail"HABfans.email "Can@22:44:45, 22.0C, 12% humidity, 14.8psia, 15.744V, 0.384A, 0.390A avg, 6.04W\\nCTD@22:45:23, 22.0495C, 0.010 decibars, 0.0000 S/m, -1.58 mg/m^3, 94.76%, 0.215 1/m\\nISUS@22:45:46, 12.350 uM/L no^3, -1.000 uM/L hs, 32.5700 psu",:Subject=>"hab sampling at most 100.0ml, wcr at most 50.0ml"

#"sh2"Lights, camera, ACTION!
#"psFlush"Flushing Processing stage 2 times
#"sh2"\PuckCamera: snap -bin=1,1 160 /var/log/esp/hires/hab08oct0700h100ml160s.tif
#"psFlush"Waiting for sh2 to relinquish FlushPuck
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/hab08oct0700h100ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40 /var/log/esp/hab08oct0700h100ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/hab08oct0700h100ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/hab08oct0700h100ml.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 56.113 seconds\
/var/log/esp/midres/hab08oct0700h100ml.tif: TIFF Upload Complete\

.\Sleepy.power :camera,:OFF

."Qmail"HABfans.email "56.113 sec auto-exposure",:Subject=>"hab08oct0700h100ml images!"

."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"

."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"

."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"

."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"

."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"

."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"

."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"

#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"

."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"

#"brent 7096"\Session Begun
{noformat}
]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop

h3. Parsing Rules

A normal flow of a log file might then look like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}

h3. Important log entries

h5. Mission start
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 3\\n Ending Wed Oct 28 08:00:00 PDT 2009",:Subject=>"09sep29moe begun"
{noformat}

h5. Whole Cell Archive starting
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; rnalwcr (1000); mfbFinalPurge :waste2b\\n/home/esp/esp2local/mission/09sep29moe.rb:11",:Subject=>"Asleep until 15:13"
{noformat}

h5. Whole Cell Archive running (by itself):
{noformat}
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"collectSample 1000ml w/bubble point of 70psi
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  1000.0ml
#collectSample: Complete
{noformat}

h5. PCR with WCR Staring
{noformat}
."Qmail"GoodNews.email "Then, in tube 3:  initialPurge; bacSHAmfb [1000,1000]\\n/home/esp/esp2local/mission/09sep29moe.rb:27",:Subject=>"Asleep until 05:13"
{noformat}

h5. PCR with WCR Running
{noformat}
#tpcr sampling at most 1000ml, wcr at most 1000ml
#tcollectSample 1000ml w/bubble point of 70psi
#t\Sampling 1000.0ml
#t\Sampled  575.3ml
#collectSample: Complete
#"WCR"Whole Cell Archive sampling 1000ml
#"WCR"\Sampling 1000.0ml
#"WCR"\Sampled  875.6ml
#collectSample: Complete
{noformat}

h5. Other

{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"

."Qmail"HABfans.email "Can@22:44:45, 22.0C, 12% humidity, 14.8psia, 15.744V, 0.384A, 0.390A avg, 6.04W\\nCTD@22:45:23, 22.0495C, 0.010 decibars, 0.0000 S/m, -1.58 mg/m^3, 94.76%, 0.215 1/m\\nISUS@22:45:46, 12.350 uM/L no^3, -1.000 uM/L hs, 32.5700 psu",:Subject=>"hab sampling at most 100.0ml, wcr at most 50.0ml"

#"sh2"Lights, camera, ACTION!
#"psFlush"Flushing Processing stage 2 times
#"sh2"\PuckCamera: snap -bin=1,1 160 /var/log/esp/hires/hab08oct0700h100ml160s.tif
#"psFlush"Waiting for sh2 to relinquish FlushPuck
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/hab08oct0700h100ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40 /var/log/esp/hab08oct0700h100ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/hab08oct0700h100ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/hab08oct0700h100ml.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 56.113 seconds\
/var/log/esp/midres/hab08oct0700h100ml.tif: TIFF Upload Complete\

.\Sleepy.power :camera,:OFF

."Qmail"HABfans.email "56.113 sec auto-exposure",:Subject=>"hab08oct0700h100ml images!"

."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"

."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"

."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"

."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"

."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"

."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"

."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"

#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"

."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"

#"brent 7096"\Session Begun
{noformat}
]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began

*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).
Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays
Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

MELO used was #300034012090780

location reported by MELO was-\- &nbsp; 33.4865 \-118.51285

*March 20*\--lost comms

*March 21*\--re-established comms and think problem in E/M cable.

*March 22*\--lost comms

*April 3*\--small boat to buoy to test E/M cable

*April 8*\--'rescue' mission. Swapped E/M cables and repositioned in slightly deeper water, at 33.48504 \-118.50988

h4. {color:#ff00cc}ECOHAB--S. California{color}

*April 1*\--Instruments deployed

&nbsp;MOE--inshore at 33.60779 \-118.01877 with ISUS

Melo was 300234060014550

avg can depth \~9m
\\

&nbsp;Bruce--offshore at 33.58609 \-118.03686

Melo was 300234060016190

avg can depth \~19.5m

*~ April 9* lost communication with Bruce.&nbsp;

*April 15*\--Rescue mission w/Nerissa found 'hung' modem.&nbsp; Power cycled and checked cables on deck.&nbsp; Re-deployed in nearby spot.&nbsp; Divers (Kim R. & George M) measured 17.7m to top of can, 25.3 m to master link.]]></property>
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<property name="body"><![CDATA[Distribution list as of 03 Mar 2010:
\\
\\
|| MFB || PCR Module # || on Core || who gets? || ||
| tombstone | 3 | NEO \\ | MBARI | |
| MFB1 | 1 | Moe | MBARI | |
| MFB2 | 5 | Betty | MBARI | |
| MFB3 | 4 | Gordon | MBARI | |
| MFB4 | 7 | | CMORE | |
| MFB5 | 8 | | U. of Ga\\ | |
| MFB6 | 13 | | Stanford | |
| MFB7 | 9 | | Harvard/Girgius | |
| MFB8 | none | | Harban's | |
| MFB9 | 10 | | Caltech/Orphan | |
| MFB10 | 11 | | SCCWRP | |
| {color:#3366ff}&nbsp;MFB11{color} | 12 | | MBARI | under construction \\ |
| | | | | |
| | Spare: | | | |
| | 14 | | | |]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop

h3. Parsing Rules

A normal flow of a log file might then look like:

{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}

h3. Important log entries
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"

."Qmail"HABfans.email "Can@22:44:45, 22.0C, 12% humidity, 14.8psia, 15.744V, 0.384A, 0.390A avg, 6.04W\\nCTD@22:45:23, 22.0495C, 0.010 decibars, 0.0000 S/m, -1.58 mg/m^3, 94.76%, 0.215 1/m\\nISUS@22:45:46, 12.350 uM/L no^3, -1.000 uM/L hs, 32.5700 psu",:Subject=>"hab sampling at most 100.0ml, wcr at most 50.0ml"

#"sh2"Lights, camera, ACTION!
#"psFlush"Flushing Processing stage 2 times
#"sh2"\PuckCamera: snap -bin=1,1 160 /var/log/esp/hires/hab08oct0700h100ml160s.tif
#"psFlush"Waiting for sh2 to relinquish FlushPuck
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 1392x1040 pixel 16-bit image for 160 seconds\
/var/log/esp/hires/hab08oct0700h100ml160s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 40 /var/log/esp/hab08oct0700h100ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 40 seconds\
/var/log/esp/hab08oct0700h100ml40s.tif: TIFF Upload Complete\

#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/hab08oct0700h100ml.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera\
Exposing 696x520 pixel 16-bit image for 56.113 seconds\
/var/log/esp/midres/hab08oct0700h100ml.tif: TIFF Upload Complete\

.\Sleepy.power :camera,:OFF

."Qmail"HABfans.email "56.113 sec auto-exposure",:Subject=>"hab08oct0700h100ml images!"

."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"

."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"

."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"

."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"

."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"

."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"

."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"

#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"

."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"

#"brent 7096"\Session Begun
{noformat}
]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">11796554</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">11829429</id>
<property name="body"><![CDATA[Here are some links to information that was important during the design of the GUI:

h5. General Swing
# [A Visual Guide to Swing Components|http://java.sun.com/docs/books/tutorial/ui/features/components.html]
# [Laying Out Components Within a Container|http://java.sun.com/docs/books/tutorial/uiswing/layout/]
# [How to Use Split Panes|http://java.sun.com/docs/books/tutorial/uiswing/components/splitpane.html]

h5. JGoodies Forms
# [JGoodies Forms FAQ|https://forms.dev.java.net/faq.html]
# [The JGoodies Forms Framework (PDF)|http://www.jgoodies.com/articles/forms.pdf]
# [JGoodies Forms Tutorial - Introduction|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/introduction.html]
# [JGoodies Forms Tutorial - Basics|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/basics.html]
# [JGoodies Forms Tutorial - Quick Start|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/quickstart.html]
# [JGoodies Forms Tutorial - Building|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/building.html]
# [JGoodies Forms Tutorial - Factories|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/factories.html]
# [JGoodies Forms References|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/references.html]
# [JGoodies Forms Tips and Tricks|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tips.html]

h5. MiGCalendar
# [JavaBeans Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/JavaBeans%20Guide.pdf]
# [Getting Started Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Getting%20Started.pdf]
# [AShape Developers Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/AShape%20Developers%20Guide.pdf]
# [FAQ|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/FAQ.pdf]
# [MiG Calendar Tutorial (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/MiG%20Calendar%20Tutorial.pdf]
# [Running the Examples (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Runnig%20Examples.pdf]
# [Themes Developer's Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Themes%20Developers%20Guide.pdf]
# [JavaDocs|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/JavaDoc/index.html]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">11796670</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">11829430</id>
<property name="body"><![CDATA[Here are some links to information that was important during the design of the GUI:

h5. General Swing
# [A Visual Guide to Swing Components|http://java.sun.com/docs/books/tutorial/ui/features/components.html]
# [Laying Out Components Within a Container|http://java.sun.com/docs/books/tutorial/uiswing/layout/]
# [How to Use Split Panes|http://java.sun.com/docs/books/tutorial/uiswing/components/splitpane.html]
# [Threads and Swing|http://java.sun.com/products/jfc/tsc/articles/threads/threads1.html]

h5. JGoodies Forms
# [JGoodies Forms FAQ|https://forms.dev.java.net/faq.html]
# [The JGoodies Forms Framework (PDF)|http://www.jgoodies.com/articles/forms.pdf]
# [JGoodies Forms Tutorial - Introduction|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/introduction.html]
# [JGoodies Forms Tutorial - Basics|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/basics.html]
# [JGoodies Forms Tutorial - Quick Start|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/quickstart.html]
# [JGoodies Forms Tutorial - Building|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/building.html]
# [JGoodies Forms Tutorial - Factories|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/factories.html]
# [JGoodies Forms References|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/references.html]
# [JGoodies Forms Tips and Tricks|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tips.html]

h5. MiGCalendar
# [JavaBeans Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/JavaBeans%20Guide.pdf]
# [Getting Started Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Getting%20Started.pdf]
# [AShape Developers Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/AShape%20Developers%20Guide.pdf]
# [FAQ|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/FAQ.pdf]
# [MiG Calendar Tutorial (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/MiG%20Calendar%20Tutorial.pdf]
# [Running the Examples (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Runnig%20Examples.pdf]
# [Themes Developer's Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Themes%20Developers%20Guide.pdf]
# [JavaDocs|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/JavaDoc/index.html]

h5. XTide
# [A Brief Introduction to XTide|http://www.linuxjournal.com/article/196]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">11796671</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">11829432</id>
<property name="body"><![CDATA[Here are some links to information that was important during the design of the GUI:

h5. General Swing
# [A Visual Guide to Swing Components|http://java.sun.com/docs/books/tutorial/ui/features/components.html]
# [Laying Out Components Within a Container|http://java.sun.com/docs/books/tutorial/uiswing/layout/]
# [How to Use Split Panes|http://java.sun.com/docs/books/tutorial/uiswing/components/splitpane.html]
# [Threads and Swing|http://java.sun.com/products/jfc/tsc/articles/threads/threads1.html]

h5. JGoodies Forms
# [JGoodies Forms FAQ|https://forms.dev.java.net/faq.html]
# [The JGoodies Forms Framework (PDF)|http://www.jgoodies.com/articles/forms.pdf]
# [JGoodies Forms Tutorial - Introduction|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/introduction.html]
# [JGoodies Forms Tutorial - Basics|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/basics.html]
# [JGoodies Forms Tutorial - Quick Start|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/quickstart.html]
# [JGoodies Forms Tutorial - Building|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/building.html]
# [JGoodies Forms Tutorial - Factories|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/factories.html]
# [JGoodies Forms References|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/references.html]
# [JGoodies Forms Tips and Tricks|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tips.html]

h5. MiGCalendar
# [JavaBeans Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/JavaBeans%20Guide.pdf]
# [Getting Started Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Getting%20Started.pdf]
# [AShape Developers Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/AShape%20Developers%20Guide.pdf]
# [FAQ|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/FAQ.pdf]
# [MiG Calendar Tutorial (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/MiG%20Calendar%20Tutorial.pdf]
# [Running the Examples (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Runnig%20Examples.pdf]
# [Themes Developer's Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Themes%20Developers%20Guide.pdf]
# [JavaDocs|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/JavaDoc/index.html]

h5. XTide
# [XTide Web Site|http://www.flaterco.com/xtide/]
# [A Brief Introduction to XTide|http://www.linuxjournal.com/article/196]]]></property>
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<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught against the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h4. A. [Cawthron Planning Document]


h4. B. [Cawthron Shipping details]

{color:#000000}March 19--E{color}SP Sea-van leaves MBARI for Oakland

{color:#000000}March 20 -{color}\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight.

March 25--Chris P and Kevan fly to NZ.&nbsp; April 5 Brent flies to NZ.

March 29 \-\- two cores, supply box and dry shipper arrive

April 22 \-\- Scott flies to NZ.

April 24 \-\- ESP Sea-van arrives at Cawthron

h4. +May 1 \-\- Deployed ESP-Gordon with MFB10, ISUS, and CTD.+

May 3 \-\- team returns to MBARI.
\\

h4. +May 31--Gordon recovered from Tasman Bay.&nbsp; Waiting for Chris P arrival and uncanning.+


June 1 \-\- Uncanned Gordon.&nbsp; Sub1 valve makes weak flubbing sound, not nice strong click. No sub getting to the arrays; this explains their darkness.


h3. {color:#ff00ff}WHOI Deployment of ESP-Chris{color}

April 15 \-\- Roman flies to WHOI; returns May 5

May 2 \-\- Deploy ESP-Chris

June 4 \-\- Discover intake syringe mechanism has failed; jams under load but works fine when moving air.&nbsp; This came after only pulling 300ml on most recent run.&nbsp; Recommend shutting down and recovering.\\]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]
# [Feb 16]
# Feb 23 \-\- Oceans Mtg., Portland
# [Mar 2]
# [Mar 9]
# Mar 16 \-\- Jim in S. Cal scouting.  John Ryan ran mtg.]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[Here are some links to information that was important during the design of the GUI:

# [A Visual Guide to Swing Components|http://java.sun.com/docs/books/tutorial/ui/features/components.html]
# [Laying Out Components Within a Container|http://java.sun.com/docs/books/tutorial/uiswing/layout/]
# [JGoodies Forms FAQ|https://forms.dev.java.net/faq.html]
# [The JGoodies Forms Framework (PDF)|http://www.jgoodies.com/articles/forms.pdf]
# [JGoodies Forms Tutorial - Introduction|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/introduction.html]
# [JGoodies Forms Tutorial - Basics|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/basics.html]
# [JGoodies Forms Tutorial - Quick Start|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/quickstart.html]
# [JGoodies Forms Tutorial - Building|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/building.html]
# [JGoodies Forms Tutorial - Factories|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/factories.html]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 18 Feb 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [MFB-PCR distribution list] as of 03Mar2010]]></property>
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<property name="body"><![CDATA[Distribution list as of 03 Mar 2010:
\\
\\
|| MFB || PCR Module # || on Core || who gets? || ||
| tombstone | 3 | NEO \\ | MBARI | |
| MFB1 | 1 | Moe | MBARI | |
| MFB2 | 5 | Betty | MBARI | |
| MFB3 | 4 | Gordon | MBARI | |
| MFB4 | 7 | | CMORE | |
| MFB5 | 8 | | U. of Ga \\ | |
| MFB6 | \\ | | Stanford | |
| MFB7 | 9 | | Harvard/Girgius | |
| MFB8 | none | | Harban's | |
| MFB9 | 13\\ | | Caltech/Orphan | |
| MFB10 | 11 | | SCCWRP | |
| {color:#3366ff}&nbsp;MFB11{color} | 12 | | MBARI | under construction \\ |
| | | | | |
| | Spare: | | | |
| | 14 | | | |
| | 10 | | bleach leak caused connector to become flakey\\ | |]]></property>
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<property name="body"><![CDATA[Here are some links to information that was important during the design of the GUI:

h5. General Swing
# [A Visual Guide to Swing Components|http://java.sun.com/docs/books/tutorial/ui/features/components.html]
# [Laying Out Components Within a Container|http://java.sun.com/docs/books/tutorial/uiswing/layout/]
# [How to Use Split Panes|http://java.sun.com/docs/books/tutorial/uiswing/components/splitpane.html]

h5. JGoodies Forms
# [JGoodies Forms FAQ|https://forms.dev.java.net/faq.html]
# [The JGoodies Forms Framework (PDF)|http://www.jgoodies.com/articles/forms.pdf]
# [JGoodies Forms Tutorial - Introduction|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/introduction.html]
# [JGoodies Forms Tutorial - Basics|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/basics.html]
# [JGoodies Forms Tutorial - Quick Start|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/quickstart.html]
# [JGoodies Forms Tutorial - Building|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/building.html]
# [JGoodies Forms Tutorial - Factories|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/factories.html]

h5. MiGCalendar
# [JavaBeans Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/JavaBeans%20Guide.pdf]
# [Getting Started Guide|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Getting%20Started.pdf]
# [JavaDocs|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/JavaDoc/index.html]]]></property>
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</property>
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<property name="body"><![CDATA[Here are some links to information that was important during the design of the GUI:

# [A Visual Guide to Swing Components|http://java.sun.com/docs/books/tutorial/ui/features/components.html]
# [Laying Out Components Within a Container|http://java.sun.com/docs/books/tutorial/uiswing/layout/]
# [How to Use Split Panes|http://java.sun.com/docs/books/tutorial/uiswing/components/splitpane.html]
# [JGoodies Forms FAQ|https://forms.dev.java.net/faq.html]
# [The JGoodies Forms Framework (PDF)|http://www.jgoodies.com/articles/forms.pdf]
# [JGoodies Forms Tutorial - Introduction|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/introduction.html]
# [JGoodies Forms Tutorial - Basics|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/basics.html]
# [JGoodies Forms Tutorial - Quick Start|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/quickstart.html]
# [JGoodies Forms Tutorial - Building|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/building.html]
# [JGoodies Forms Tutorial - Factories|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/factories.html]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">11796657</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[Here are some links to information that was important during the design of the GUI:

h5. General Swing
# [A Visual Guide to Swing Components|http://java.sun.com/docs/books/tutorial/ui/features/components.html]
# [Laying Out Components Within a Container|http://java.sun.com/docs/books/tutorial/uiswing/layout/]
# [How to Use Split Panes|http://java.sun.com/docs/books/tutorial/uiswing/components/splitpane.html]

h5. JGoodies Forms
# [JGoodies Forms FAQ|https://forms.dev.java.net/faq.html]
# [The JGoodies Forms Framework (PDF)|http://www.jgoodies.com/articles/forms.pdf]
# [JGoodies Forms Tutorial - Introduction|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/introduction.html]
# [JGoodies Forms Tutorial - Basics|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/basics.html]
# [JGoodies Forms Tutorial - Quick Start|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/quickstart.html]
# [JGoodies Forms Tutorial - Building|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/building.html]
# [JGoodies Forms Tutorial - Factories|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/factories.html]
# [JGoodies Forms References|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/references.html]

h5. MiGCalendar
# [JavaBeans Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/JavaBeans%20Guide.pdf]
# [Getting Started Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Getting%20Started.pdf]
# [AShape Developers Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/AShape%20Developers%20Guide.pdf]
# [FAQ|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/FAQ.pdf]
# [MiG Calendar Tutorial (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/MiG%20Calendar%20Tutorial.pdf]
# [Running the Examples (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Runnig%20Examples.pdf]
# [Themes Developer's Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Themes%20Developers%20Guide.pdf]
# [JavaDocs|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/JavaDoc/index.html]]]></property>
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<property name="body"><![CDATA[Here are some links to information that was important during the design of the GUI:

h5. General Swing
# [A Visual Guide to Swing Components|http://java.sun.com/docs/books/tutorial/ui/features/components.html]
# [Laying Out Components Within a Container|http://java.sun.com/docs/books/tutorial/uiswing/layout/]
# [How to Use Split Panes|http://java.sun.com/docs/books/tutorial/uiswing/components/splitpane.html]

h5. JGoodies Forms
# [JGoodies Forms FAQ|https://forms.dev.java.net/faq.html]
# [The JGoodies Forms Framework (PDF)|http://www.jgoodies.com/articles/forms.pdf]
# [JGoodies Forms Tutorial - Introduction|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/introduction.html]
# [JGoodies Forms Tutorial - Basics|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/basics.html]
# [JGoodies Forms Tutorial - Quick Start|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/quickstart.html]
# [JGoodies Forms Tutorial - Building|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/building.html]
# [JGoodies Forms Tutorial - Factories|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/factories.html]

h5. MiGCalendar
# [JavaBeans Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/JavaBeans%20Guide.pdf]
# [Getting Started Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Getting%20Started.pdf]
# [AShape Developers Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/AShape%20Developers%20Guide.pdf]
# [FAQ|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/FAQ.pdf]
# [MiG Calendar Tutorial (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/MiG%20Calendar%20Tutorial.pdf]
# [JavaDocs|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/JavaDoc/index.html]]]></property>
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<property name="body"><![CDATA[Email from Scott, January 9, 2008 (updated 1-15-2008):&nbsp;

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note that we have yet to make a full batch of high-volume snap pucks, but when we do, those will be labeled 1HV (top and bottom).

Here is who is doing our etching:

LaserMark
2109 O'Toole Ave. Ste S
San Jose, CA 95131
Phone 408 433-9333
Fax 408 433-9343
\\
\\

Here is what I have packed up for etching:
| Type | Top/bottom | Numbered | Amount | NOTE |
| WCR | Top | 040-079 | 40 | \\ |
| \\ | Bottom | 040-079 | 40 | \\ |
| LAF | Top | 040-078 | 39 | 1=Missing |
| \\ | Bottom | 040-078 | 39 | 1=Missing |
| SAF | Top | 040-075 | 36 | 4sent to Gregg D |
| \\ | Bottom | 040-075 | 36 | 4sent to Gregg D |
| SHT | Top | 080-159 | 80 | \\ |
| SH1 | Bottom | 080-159 | 80 | \\ |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 390 | \\ |
\\
\\

I also sent 1 WCR puck (top&bottom) as a font sample.&nbsp; When these come back I will pack up the ones that are to be re-numbered(SHT2000-079).&nbsp; I haven't received a quote yet but Laser Mark said about $2 each piece + shipping.
\\

3/24/08

The SH1 tops that were misprinted are going to be sent out tomorrow to be re etched along with one of the LAF's that escaped detection last time:
| Type | Top/bottom | Numbered | Amount | NOTE |
| LAF | Top | 079 | 1 | Found the Lost 1\! |
| \\ | Bottom | 079 | 1 | \\ |
| SHT | Top | 000-079 | 80 | Old etching to be X'd out |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 82 | \\ |
That is all for now\\ \\ \\

2/24/09&nbsp; There have been several iterations of the above serialization process since this was last updated.&nbsp; Here is where we now stand:
| This   is an inventory of pucks that have been serialized and are available for   use.&nbsp; | \\ | \\ | \\ |
| There are   aprox. 1200 more pieces (or 600 more pucks) that have yet to be serialized. | \\ | \\ |
| They are   located in the 'B' building lab | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| Type | Top/Bottom | Lot 2 | Lot 2 | Lot 3 | Lot 3 | Lot 4 | Total | \\ |
| WCR | Top | 40 | 40 | 40 | 39 | 40 | 199 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 40 | 40 | 200 | \\ |
| LAF | Top | 40 | 40 | 40 | 38 | 40 | 198 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 36 | 40 | 196 | \\ |
| SAF | Top | 40 | 36 | 40 | 39 | 40 | 195 | \\ |
| \\ | Bottom | 40 | 36 | 40 | 40 | 40 | 196 | \\ |
| SHT | Top | 80 | 80 | 80 | 80 | 80 | 400 | \\ |
| SH1\\ | Bottom | 80 | 80 | 80 | 77 | 80 | 397 | \\ |
| Total | \\ | 400 | 392 | 400 | 389 | 400 | 1981 | 990.5 |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | pieces | pucks |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| The   lot number refers to the 4th place in the serialization code:&nbsp; | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 letter type | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 1 digit lot number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 digit individual part number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| All parts   are numbered 000-079 ( except where some are missing) for each lot EXCEPT for : | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SHT=000-159 | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SH1=000-159 | \\ | \\ | \\ | \\ |]]></property>
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<property name="body"><![CDATA[\\

h2. American Portable Storage

Oakland, CA
1-800-838-4006&nbsp;&nbsp; &nbsp;(Ken)

220V single phase (newer; quiet)
Delivery/pickup $850
$650/mo w/ 2 mo min.&nbsp; Uses $95/mo electricity.

220V 3-phase
$600/mo.&nbsp; Older noisy.&nbsp; Uses $450/mo electricity.

THIS IS THE COMPANY WE PURCHASED FROM.

Michael McCurley--his quote is [here|^MBARI Quote.doc].

Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].

PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)


h2. Aztec Containers

Stockton, CA
1-800-399-2126 (Mark)

220 3-phase
Delivery/pickup $495
$695/mo w/ 3 mo min.

h2. Refrigerated Container Services

Oakland, CA
1-510-568-9541

220 3-phase
delivery/pickup \~$500
$1000/mo w/ no minimum.

Could purchase for \~$7800.&nbsp; They may repurchase for ½ price after we're finished.

Reefers only have doors on one end.&nbsp; No lights.&nbsp; Pass-throughs?&nbsp; Unknown.]]></property>
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<property name="body"><![CDATA[Distribution list as of 05 Apr 2010:
\\
\\
|| MFB || PCR Module # || on Core || who gets? || ||
| tombstone | 9 \\ | NEO \\ | MBARI | |
| MFB1 | 1 | Moe | MBARI | |
| MFB2 | 5 | Betty | MBARI | |
| MFB3 | 4 | Gordon | MBARI | |
| MFB4 | 7 \\ | | CMORE | |
| MFB5 | 8 | | U. of Ga \\ | |
| MFB6 | 10 \\ | | Stanford | bleach leak causes flakey connector? |
| MFB7 | | | Harvard/Girgius | |
| MFB8 | none | | Harban's | |
| MFB9 | 13 \\ | | Caltech/Orphan | |
| MFB10 | 11 | | SCCWRP | |
| {color:#3366ff}&nbsp;MFB11{color} | 12 | | MBARI | under construction \\ |
| | | | | |
| | Spare: | | | |
| | 14 | | | |
| | | | \\ | |
| | 3 | | was originally on Tombstone, but moved #7 there for M0 deployment \\ | |]]></property>
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<property name="body"><![CDATA[Distribution list as of 05 Apr 2010:
\\
\\
|| MFB || PCR Module # || on Core || who gets? || ||
| tombstone | 7\\ | NEO \\ | MBARI | |
| MFB1 | 1 | Moe | MBARI | |
| MFB2 | 5 | Betty | MBARI | |
| MFB3 | 4 | Gordon | MBARI | |
| MFB4 | \\ | | CMORE | |
| MFB5 | 8 | | U. of Ga \\ | |
| MFB6 | \\ | | Stanford | |
| MFB7 | 9 | | Harvard/Girgius | |
| MFB8 | none | | Harban's | |
| MFB9 | 13 \\ | | Caltech/Orphan | |
| MFB10 | 11 | | SCCWRP | |
| {color:#3366ff}&nbsp;MFB11{color} | 12 | | MBARI | under construction \\ |
| | | | | |
| | Spare: | | | |
| | 14 | | | |
| | 10 | | bleach leak caused connector to become flakey \\ | |
| | 3 | | was originally on Tombstone, but moved #7 there for M0 deployment\\ | |]]></property>
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<property name="body"><![CDATA[Here are some links to information that was important during the design of the GUI:

h5. General Swing
# [A Visual Guide to Swing Components|http://java.sun.com/docs/books/tutorial/ui/features/components.html]
# [Laying Out Components Within a Container|http://java.sun.com/docs/books/tutorial/uiswing/layout/]
# [How to Use Split Panes|http://java.sun.com/docs/books/tutorial/uiswing/components/splitpane.html]

h5. JGoodies Forms
# [JGoodies Forms FAQ|https://forms.dev.java.net/faq.html]
# [The JGoodies Forms Framework (PDF)|http://www.jgoodies.com/articles/forms.pdf]
# [JGoodies Forms Tutorial - Introduction|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/introduction.html]
# [JGoodies Forms Tutorial - Basics|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/basics.html]
# [JGoodies Forms Tutorial - Quick Start|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/quickstart.html]
# [JGoodies Forms Tutorial - Building|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/building.html]
# [JGoodies Forms Tutorial - Factories|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/factories.html]
# [JGoodies Forms References|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/references.html]
# [JGoodies Forms Tips and Tricks|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tips.html

h5. MiGCalendar
# [JavaBeans Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/JavaBeans%20Guide.pdf]
# [Getting Started Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Getting%20Started.pdf]
# [AShape Developers Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/AShape%20Developers%20Guide.pdf]
# [FAQ|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/FAQ.pdf]
# [MiG Calendar Tutorial (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/MiG%20Calendar%20Tutorial.pdf]
# [Running the Examples (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Runnig%20Examples.pdf]
# [Themes Developer's Guide (PDF)|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/doc/Themes%20Developers%20Guide.pdf]
# [JavaDocs|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/MiGInfo%20Calendar/6.8.6/JavaDoc/index.html]]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">11796643</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">11829381</id>
<property name="body"><![CDATA[Here are some links to information that was important during the design of the GUI:

# [A Visual Guide to Swing Components|http://java.sun.com/docs/books/tutorial/ui/features/components.html]
# [Laying Out Components Within a Container|http://java.sun.com/docs/books/tutorial/uiswing/layout/]
# [JGoodies Forms FAQ|https://forms.dev.java.net/faq.html]
# [The JGoodies Forms Framework (PDF)|http://www.jgoodies.com/articles/forms.pdf]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">11796622</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">11829383</id>
<property name="body"><![CDATA[Here are some links to information that was important during the design of the GUI:

# [A Visual Guide to Swing Components|http://java.sun.com/docs/books/tutorial/ui/features/components.html]
# [Laying Out Components Within a Container|http://java.sun.com/docs/books/tutorial/uiswing/layout/]
# [JGoodies Forms FAQ|https://forms.dev.java.net/faq.html]
# [The JGoodies Forms Framework (PDF)|http://www.jgoodies.com/articles/forms.pdf]
# [JGoodies Forms Tutorial - Introduction|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/introduction.html]
# [JGoodies Forms Tutorial - Basics|https://alfresco.mbari.org/alfresco/webdav/Engineering/Software%20Engineering/Computer/Programming/Languages/Java/Libraries/JGoodies/forms-1.3.0/docs/tutorial/basics.html]]]></property>
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<property name="body"><![CDATA[h4. (as of April, 2015)


h1. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

*21.5m (BAD)*
Now with bad connector...&nbsp;
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos in the attachments of this page.

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)

*15.2m (BAD; bad BSR?)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]

Shockles were first used on the New Zealand Cawthron deployment in March, 2012.

(shockles 1-4 used in SoCal ECOHAB-2013 and Monterey Bay ECOHAB-2013, but unclear which used when )\\

All shockles modified Dec 2015 to be like 001 (stretchier cords)


h4. ESP-001 (modified with 'stretchier' cord)

* 44 days during Catalina (April 2014) deployment
* Moran MB deployment (Sep/Oct 2014)
* ECOHAB?

h4. ESP-002


h4. ESP-003


h4. ESP-004


h4. ESP-005


h1. Anchor lines

\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4.


h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\
\\]]></property>
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<property name="body"><![CDATA[h4. (as of April, 2015)


h1. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

*21.5m (BAD)*
Now with bad connector...&nbsp;
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos in the attachments of this page.

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)

*15.2m (BAD; bad BSR?)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]

Shockles were first used on the New Zealand Cawthron deployment in March, 2012.


(shockles 1-4 used in SoCal ECOHAB-2013 and Monterey Bay ECOHAB-2013, but unclear which used when )

h4. ESP-001 (modified with 'stretchier' cord)

* 44 days during Catalina (April 2014) deployment
* Moran MB deployment (Sep/Oct 2014)
* ECOHAB?

h4. ESP-002

\\

h4. ESP-003

* &nbsp;32 days S. Cal ECOHAB w/Mack (Apr 2014)

h4. ESP-004

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).

h4. ESP-005


h1. Anchor lines

\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4.


h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\
\\]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

April 2, 2010.&nbsp; So. Cal beginning.

Bruce (water = 55m)
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7" ]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">15663586</id>
<property name="body"><![CDATA[# [Science Meetings]
# [Engineering Meetings]
# [Software Development Meetings]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">15630829</id>
</property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes (no longer maintained--Sep 2012)

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
# [2014 Deployments]
# [2015 Deployments]
# [2016 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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</property>
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<id name="id">15663589</id>
<property name="body"><![CDATA[h1. All dates 2011

# &nbsp;Jan 4
# &nbsp;\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">15630832</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">28672394</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes (no longer maintained--Sep 2012)

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments](MB)
# [2009 Deployments](MB, MARS, SC Wharf)
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
# [2014 Deployments]
# [2015 Deployments]
# [2016 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h4.


h4. {color:#ff00cc}SCRIPPS-Lab Run \-\- ESP-Waldo{color}

*&nbsp;April 27, 2015*

Roman delivers ESP Waldo to Andy Allen's lab at CVGI.&nbsp; Idea was to collect archived sample twice/week for \~6 months to test longevity issues with filters.

mid-June, instrument started losing comms to elevator dwarf.&nbsp; Roman sent down to replace dwarf on June 29-30. Re-canned and restarted mission.

RECOVERY

Roman recovers ESP-Waldo October 6, 2015.

h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce. Divers: Kim R., Paul C.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

Divers: Paul C., Jeff Sevadjian

{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload. Divers: Eric R, Jeff Sevadjian
\\

h4. {color:#ff00cc}1st MAKAI flight w 5 cartridges{color}

*July 22, 2015*

Flew triangle pattern after launch.&nbsp; Makai found chlorophyll feature, and we fired two cartridges while flying through.&nbsp; First cartridge may have had sticky valve and stayed in by-pass (filtered 1L in \~20 minutes; too fast).&nbsp; Second cartridge seemed to have worked.

Some issues with ESP not communicating it was on, and then LRAUV not turning it on.&nbsp; Went to recover vehicle late July 23, but did not surface until mission timed-out, after we were already ashore.&nbsp; That was when we discovered the comms issues.&nbsp; Fixed one, tried to fire during a 'night operation' Thursday evening.&nbsp; Discovered Friday morning a second comms issues, which was fixed, and fired the 3 samples during day on Friday, July 24.&nbsp; Did keep-station all weekend, and recovered LRAUV early Monday morning (July 27).

Results:

1.&nbsp; Cartridge #1 bypassed 1L (toroid valve stuck; sea water ran through instrument in bypass mode; 7 minutes); flying through feature (chl=3.0 ug/l; 10.97m)

2. &nbsp; #2 filtered 815.8ml; flying through feature (11.03m; chl=3.3 ug/l; took 53 minutes)

3. &nbsp; #3 filtered 802.3ml;&nbsp; within feature (13.8m; chl=3.02 ug/l; took 51 minutes)

4. &nbsp; #4 filtered 759.6ml,&nbsp; above feature (7.1m; chl=1.11 ug/l; took 50 minutes)

5.&nbsp;&nbsp; #5 filtered 809.1ml,&nbsp; below feature (19.4m; chl=4.24 ug/l; took 51 minutes)

Excellent summary paper by Yanwu Zhang about what the LRAUV did during this deployment-\-[here|^Zhang_etal_chlpeak.pdf|Yanwu's paper].(check your download folder)

h4. {color:#ff00cc}SCRIPPS-Del Mar Mooring \-\- ESP-Waldo{color}

*&nbsp;November 12, 2015*

Roman and Scott drive down Nov 8 and work for the week to assemble mooring.&nbsp; Goes in water on the 12th (check ESP-Waldo channel on Slack for pictures).&nbsp; Setup has SCRIPPS modem as master mooring controller.&nbsp; when it sends command string to ESP, ESP and ESP-modem awake, which allows us to get into ESP for diagnosis and large data transfers.&nbsp; At end of sampling, ESP and it's modem goes to sleep.&nbsp; Currently (Dec 1) using [this|^ESP deploy _DelMar_sampling_127.xlsx|Sampling schedule as of Dec 1] sampling schedule.

Dec 6, 2015

I2C error has stopped our sampling mission.&nbsp; ESP now providing only CTD updates.&nbsp; Brent's message:&nbsp; "The problem that surfaced first last Wednesday has recurred and is not going away this time.

Waldo's ESP host can access the sleepy microcontroller to get can status, etc., however, sleepy cannot access anything on the I2C bus."

Dec 14, 2015

I2C bus was back online\!&nbsp; Instrument had been left 'on' since last communications, and had some rough weather over this weekend.&nbsp; Brent was able to get in and unstick the hand then take a 'flawless' sample.&nbsp; Will see how she works in four days...

*Recovered Feb 4, 2016*.


h4. {color:#ff00cc}MAKAI flight w 4 Archives, 1 Lyse-n-go{color}

*Dec 18-21, 2015*

Launch/recover from MLML rib boat.&nbsp; Multiple failures with LRAUV; difficulty holding (shallow) depth, thruster errors. Original idea was to find a chl feature, take 2 archives.&nbsp; Dive below feature, take two archives.&nbsp; Reacquire feature, fire off l-n-g.&nbsp; With multiple vehicle errors and time running out (Holiday break; people leaving) we got one shallow archive, one deep, and ran the l-n-g deep.&nbsp; No feature ever found--very stormy and little stratification. Brett, Brian, Chris P on deployment; Brett, Ben, Jim on recovery.]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
\\
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage taken by Rob Vincent:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]

Map of locations:&nbsp; [http://maps.google.com/maps/ms?ie=UTF&msa=0&msid=213220825771739778963.0004a40bdd601babc291d]

May 23.&nbsp; Attempted recovery of ESP.&nbsp; Message from Roman:

{color:#996600}&nbsp;&nbsp;&nbsp; We went out to the site where espbruce was moored and attempted to find it.&nbsp; The weather was very poor and water was very turbid.&nbsp; Using the ships depth finder we found a promising target.&nbsp; In difficult conditions the divers performed a search but espbruce was not found.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; We recovered the mooring.&nbsp; It looks like the cable was pulled straight out of the cone.&nbsp; The top mast is bent but I cannot say if this was caused by a rough landing on the beach or boat impact.&nbsp; There are no dents or gouges on the mooring.&nbsp; The radio box is dry and antenna looks ok.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; Thursday the RV Gulf Challenger may be able to survey the area with a side scanning sonar.&nbsp; This will be a much better way to search for espbruce.&nbsp;{color}

Message from Roman May 26:

{color:#996600}&nbsp;&nbsp;&nbsp; ESPbruce was located at&nbsp; 43° 02.0740 N&nbsp;&nbsp; 70° 36.8447 W at ~ 10m depth.&nbsp; This position is about 19 yards from the waypoint.&nbsp; So looks like it wasn't dragged and has maintained seal integrity.&nbsp; We will attempt to recover it this weekend if we can get the RV Tioga.&nbsp; If not will recover with the RV Connecticut on june 7th weather permitting.{color}
&nbsp;

Dates for a recovery kept moving as weather and scheduling problems arose.&nbsp; Finally, Roman reported on June 15:
{quote}
{quote}
{color:#996600}ESPbruce was recovered today with no visible external damage. The EM cable strain relief is still on the cable.&nbsp; The recovery operation used two ships the RV Gulf Challenger and it's sister the RV Tioga.&nbsp; The Challenger supported the the side scan survey and the Tioga supported the divers and lifting of the core package and its anchor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;The side scan sonar operator advised me at the beginning of the day that he believed the esp package would be found on the bottom.&nbsp; He based this opinion on the data secured by his colleague almost two weeks ago.&nbsp; From his read of that run, he believed that the instrument was 15m off the bottom at that time.&nbsp; Depth at this site is 49m.&nbsp; He felt that the instrument was slowly sinking and that by today it was surly be on the sea floor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Todays side scan survey took approximately 90 minutes.&nbsp; They had acquired a strong signature on the core and calculated that it was at a depth of 65 feet (~20m). The package&nbsp; was still located within 10m of the original deployment site.&nbsp; They dropped a marker line with a float as close to the calculated position as possible.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;At this point divers equipped with twin 80 cu ft Nitrox cylinders and electric scooters dived on the marker.&nbsp; They had 70 minutes of search time.&nbsp; After 42 minutes an orange sausage float attached to a spectra lift line appeared.&nbsp; Then 10 minutes later a second lift bag attached to the EM cable appeared.&nbsp; The divers surfaced after a total bottom time of 62 minutes.&nbsp; Eight minutes to spare.&nbsp; We recovered the divers.&nbsp; They reported that the depth of top of the can was at 26 feet (~8m) right where it was supposed to be.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Recovery went smoothly using a single winch equipped with a capstan attachment.&nbsp; By alternately shifting the load from drum (used to lift anchor) and capstan (used to lift instrument we recovered the package and the anchor safely.{color}
{quote}
\\
\\  {color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford.

{color:#cc3300}July 6{color} \-\- Ship by truck D-ESP and supplies for JdF cruise.&nbsp; To Newport, OR.

{color:#cc3300}July 13{color} \-\- Sail for Axial and JdF (1 day late due to weather getting up to Newport)

{color:#cc0000}July 20{color} \-\- recall D-ESP.&nbsp; Recover all instruments.&nbsp; Two more days for Dave Clague.&nbsp; Ship returns July 23.
\\

Aug 17 \-\- Matson picks up loaded ESP van.&nbsp; Genset on truck putting out >530V so our reefer unit will not start.&nbsp; Decide to send due to late hour and ship leaving tomorrow.&nbsp; Van wt. w/ all ESP-Drifter gear: 15,000 lbs.

Sep 9 \-\- Drifting ESP deployed from Kilo Moana N of Station Aloha.&nbsp; Running Bruce w/ MFB ?.

Sep 17 \-\- Drifting ESP recovered.&nbsp; Gear shipped Oct 7 (via DHX and Matson), arrived at MBARI Oct 12..

{color:#9900cc}Nov 2{color} \-\- Install ESP Gordon w/PCR on Santa Cruz Pier.&nbsp; no CTD/ISUS data.&nbsp; Running water quality assay Kevan Yamahara developed.

{color:#9900cc}Dec 19{color} \-\- Recover from Santa Cruz Pier ]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes (no longer maintained--Sep 2012)

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments](MB)
# [2009 Deployments](MB, MARS, SC Wharf)
# [2010 Deployments] (MB, SoCAL, Methane Mound, Drifter, MARS, SC Pier)
# [2011 Deployments](MB, GoM, Axial, Drifter-HI, SC Pier)
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments] (MB, New Zealand, SoCAL, Friday Harbor, GoM, Drifter)
# [2013 Deployments] (MB, SoCAL, MARS, Puget Sound)
# [2014 Deployments] (MB, San Diego, Catalina, SoCAL, 3G)
# [2015 Deployments] (MB, SCRIPPS, 3G)
# [2016 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
\\
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage taken by Rob Vincent:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]

Map of locations:&nbsp; [http://maps.google.com/maps/ms?ie=UTF&msa=0&msid=213220825771739778963.0004a40bdd601babc291d]

May 23.&nbsp; Attempted recovery of ESP.&nbsp; Message from Roman:

{color:#996600}&nbsp;&nbsp;&nbsp; We went out to the site where espbruce was moored and attempted to find it.&nbsp; The weather was very poor and water was very turbid.&nbsp; Using the ships depth finder we found a promising target.&nbsp; In difficult conditions the divers performed a search but espbruce was not found.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; We recovered the mooring.&nbsp; It looks like the cable was pulled straight out of the cone.&nbsp; The top mast is bent but I cannot say if this was caused by a rough landing on the beach or boat impact.&nbsp; There are no dents or gouges on the mooring.&nbsp; The radio box is dry and antenna looks ok.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; Thursday the RV Gulf Challenger may be able to survey the area with a side scanning sonar.&nbsp; This will be a much better way to search for espbruce.&nbsp;{color}

Message from Roman May 26:

{color:#996600}&nbsp;&nbsp;&nbsp; ESPbruce was located at&nbsp; 43° 02.0740 N&nbsp;&nbsp; 70° 36.8447 W at ~ 10m depth.&nbsp; This position is about 19 yards from the waypoint.&nbsp; So looks like it wasn't dragged and has maintained seal integrity.&nbsp; We will attempt to recover it this weekend if we can get the RV Tioga.&nbsp; If not will recover with the RV Connecticut on june 7th weather permitting.{color}
&nbsp;

Dates for a recovery kept moving as weather and scheduling problems arose.&nbsp; Finally, Roman reported on June 15:
{quote}
{quote}
{color:#996600}ESPbruce was recovered today with no visible external damage. The EM cable strain relief is still on the cable.&nbsp; The recovery operation used two ships the RV Gulf Challenger and it's sister the RV Tioga.&nbsp; The Challenger supported the the side scan survey and the Tioga supported the divers and lifting of the core package and its anchor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;The side scan sonar operator advised me at the beginning of the day that he believed the esp package would be found on the bottom.&nbsp; He based this opinion on the data secured by his colleague almost two weeks ago.&nbsp; From his read of that run, he believed that the instrument was 15m off the bottom at that time.&nbsp; Depth at this site is 49m.&nbsp; He felt that the instrument was slowly sinking and that by today it was surly be on the sea floor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Todays side scan survey took approximately 90 minutes.&nbsp; They had acquired a strong signature on the core and calculated that it was at a depth of 65 feet (~20m). The package&nbsp; was still located within 10m of the original deployment site.&nbsp; They dropped a marker line with a float as close to the calculated position as possible.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;At this point divers equipped with twin 80 cu ft Nitrox cylinders and electric scooters dived on the marker.&nbsp; They had 70 minutes of search time.&nbsp; After 42 minutes an orange sausage float attached to a spectra lift line appeared.&nbsp; Then 10 minutes later a second lift bag attached to the EM cable appeared.&nbsp; The divers surfaced after a total bottom time of 62 minutes.&nbsp; Eight minutes to spare.&nbsp; We recovered the divers.&nbsp; They reported that the depth of top of the can was at 26 feet (~8m) right where it was supposed to be.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Recovery went smoothly using a single winch equipped with a capstan attachment.&nbsp; By alternately shifting the load from drum (used to lift anchor) and capstan (used to lift instrument we recovered the package and the anchor safely.{color}
{quote}
\\
\\  {color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford.

{color:#cc3300}July 6{color} \-\- Ship by truck D-ESP and supplies for JdF cruise.&nbsp; To Newport, OR.

{color:#cc3300}July 13{color} \-\- Sail for Axial and JdF (1 day late due to weather getting up to Newport)

{color:#cc0000}July 20{color} \-\- recall D-ESP.&nbsp; Recover all instruments.&nbsp; Two more days for Dave Clague.&nbsp; Ship returns July 23.
\\

Aug 17 \-\- Matson picks up loaded ESP van.&nbsp; Genset on truck putting out >530V so our reefer unit will not start.&nbsp; Decide to send due to late hour and ship leaving tomorrow.&nbsp; Van wt. w/ all ESP-Drifter gear: 15,000 lbs.

Sep 9 \-\- Drifting ESP deployed from Kilo Moana N of Station Aloha.&nbsp; Running Bruce w/ MFB ?.

Sep 17 \-\- Drifting ESP recovered.&nbsp; Gear shipped Oct 7 (via DHX and Matson), arrived at MBARI Oct 12..

{color:#9900cc}Nov 2{color} \-\- Install ESP Gordon w/PCR on Santa Cruz Pier.&nbsp; no CTD/ISUS data.&nbsp; Running water quality assay Kevan Yamahara developed.

{color:#9900cc}Dec 19{color} \-\- Recover from Santa Cruz Pier ]]></property>
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<property name="body"><![CDATA[This link takes you to the latest version

[v.1.0.81|cifs://tornado.shore.mbari.org/projectlibrary/ESP/Micro&Fluidic&Blcok/Users&Manual/Gen2&MFB&manual/MFB&User&Manual&v1.0.81.pdf]


The latest MFB manual is located in the Project Library following this path:

&nbsp;//projectlibrary/ESP/Micro Fluidic Block/Users Manual/Gen2 MFB manual]]></property>
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<property name="body"><![CDATA[The latest MFB manual is located in the Project Library following this path:
&nbsp;//projectlibrary/ESP/Micro Fluidic Block/Users Manual/Gen2 MFB manual\\

Link to be added soon. ]]></property>
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<property name="body"><![CDATA[# [v. 1.0.81 |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/Gen2%20MFB%20manual/MFB%20User%20Manual%20v1.0.81.pdf]]]></property>
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<property name="body"><![CDATA[# [v. 1.0.4 |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/Gen2%20MFB%20manual/MFB%20User%20Manual%20v1.0.4.pdf]]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# &nbsp;]]></property>
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<property name="body"><![CDATA[The latest MFB manual is located in the Project Library following this path:


&nbsp;//projectlibrary/ESP/Micro Fluidic Block/Users Manual/Gen2 MFB manual
\\

Link to be added soon. ]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]
# [Apr 12] \-\- Roman at WHOI, Chris P Europe
# Apr 19
# [Apr 26]
# [May 10]
# [May 17]
# May 24 \-\- Roman at WHOI, Chris S at WHOI, Chris P out]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit+\] &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.


time_increment with no digits <+> is equivalent to \+1 tic.
\\ \\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)


&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash


&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# CVS client
# gcc
# yacc

h3. Steps to build and run

# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:
{code}
cvs checkout ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.
{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This will populate the patch directory with the ruby source files without overwriting the patches.
# Now run configure.
{code}
./configure
{code}
# Now run make.
{code}
make
{code}
# If all goes well, ruby will have built and you can install by running this as 'root'.
{code}
make install
{code}
# After that, ruby should be ready to go and if you type
{code}
ruby --version
{code}
You should see something like:
{code}
ruby 1.6.8-mbari7/0x4770 (2009-1-19) [i686-linux]
{code}
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}]]></property>
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<property name="body"><![CDATA[h3.


h3. This email discusses the changes that have to occur to have HAB arrays and qPCR from one sample event.&nbsp; It also incorporates the other possible code changes that have to occur on NEO.&nbsp; We should also keep in mind running the DA arrays in concert and how this affects the plumbing and valve moves of the PRV.

\\

1.&nbsp; Copy NEO's current Flash to Tornado

{color:#3300cc}6/14/11{color}&nbsp; Tornado/ESP/NEOtombstoneCode11jun14

2.&nbsp; Update code on NEO (Brent has already updated ruby code) and determine what is now "broken"

{color:#3300cc}6/14/11{color} moved to bufflehead.&nbsp; Use user preston.&nbsp; Problems with /var/log setup and the correct path for mounting bufflehead. If it loose home or fails use /sbin/service nfsmount start to regain connection.&nbsp; You must be a superuser.&nbsp; Brent will have to look at this when he returns.&nbsp;

3.&nbsp; Rig with Dummy MFB to make seeing core moves easier
4.&nbsp; Determine if the AIV lines (to PRV and CBV) need to be changed.
&nbsp;&nbsp; &nbsp;a.&nbsp; To match other instruments and handle the larger lysate volume generated by the HAB protocol

{color:#9933cc}6/15/11{color} With the current lines on NEO and new code only recover 700ul of lysate.&nbsp; Prime is not correct we loose too much. After CS.push to 0 the line between the PRV and PTV is completely filled with lysate which is all sent to waste.


5.&nbsp; Do we have enough lysate volume for delivery of 1ml lysate to the array and up to 250 ul for the qPCR?
&nbsp;&nbsp; &nbsp;a.&nbsp; update PRVprocess.rb to handing the priming of the larger volume (depending on length of CBV-AIV-PRV line this may effect the positioning of the lysate to the PRV for the bacSHAmfb protocol)
6.&nbsp; Update code to deliver 1ml lysate (undiluted ) to array.&nbsp; Current protocol dilutes to 1.5M GusCN for BAC array.
7.&nbsp; Create and testing of&nbsp; habSHAmfb protocol based on the structure of the bacSHAmfb
&nbsp;&nbsp; &nbsp;a.&nbsp; Start with "normal protocol"&nbsp; 250ul of lysate and 225 ul of SPEdiluent
8.&nbsp; Testing of dilution of Lysate protocol

{color:#3300cc}6/15/11&nbsp;{color} Dilution protocol will have to include a rinse of the mixloop.&nbsp; The transferPRV protocol uses the mixloop to depressurize the lines.&nbsp; Lots of concentrated lysate.
9.&nbsp; Timing of array hybridization with lysate dilution step \--incorporation into habSHAmfb and mfb protocol
&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-----update of bacSHAmfb is not necessary for Pier deployment
10.&nbsp; CC clamp has to get the heavier springs

h3. The second email Diluting Lysate for qPCR on ESP&nbsp; (Email 2 of 2)-\- is  exactly for that lysate dilution by the core prior to delivery to the  MFB.

Brent added code to pass in an optional block in the loadMFBslug protocol, which will make its implementation much easier.&nbsp; It will have to be determined if the timing of diluting the lysate fits into the current time alloted for the hybridization of the array (if one is being run on the same sample.)&nbsp; This code starts once the concentrated lysate has been primed to the PRV.

The Major steps are:

{color:#000000}0.5&nbsp; rinse of the mixloop (Could occur prior to delivery of lysate to array.){color}

1.&nbsp; Airs out mixloop line (Currently done in loadMFBslug)
2.&nbsp; Dilution of Lysate (start with 1:10 dilution).&nbsp; Pulls lysate 0.1 ml then GuSCN 0.9ml (1ml total volume), into PS via PRV-PSV line. Then fills the syringe with air from the PRV.&nbsp; Mixes the lysate.
3.&nbsp; Move the diluted lysate into mixing coil.
4.&nbsp; Rinses the PSV-PRV-AIV/CBV line, bypasses mixloop (created samplePassF--based on samplePassCa)
5.&nbsp; Moves diluted lysate held in mixing coil to the CBV-AIV line.&nbsp; Primed to PRV.valve
6.&nbsp; Mixes diluted lysate with speDil (same protocol/ratio in loadMFBslug)
7.&nbsp; Positions slug in AIV for MFB (completes loadMFBslug)

Possible Valve Configuration Change for PRV::
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; GuSCN has to be primed to valve
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; Assumes that we don't change current DA reagent positions.

A.&nbsp; With DA reagents
&nbsp;&nbsp;&nbsp; 1 AIV/CBV
&nbsp;&nbsp;&nbsp; 2 ab1
&nbsp;&nbsp;&nbsp; 3 speDil
&nbsp;&nbsp;&nbsp; 4 guscn
&nbsp;&nbsp;&nbsp; 5 Sipper // diluent?
&nbsp;&nbsp;&nbsp; 6 waste2
&nbsp;&nbsp;&nbsp; 7 ab2
&nbsp;&nbsp;&nbsp; 8 air clean
If BAC arrays are performed on samples also for qPCR, then the sipper has to be converted into diluent.

B.&nbsp; w/o DA reagents&nbsp; (Nearly same as current PRV valve with MFB attached)
&nbsp;&nbsp;&nbsp; 1 AIV/CBV
&nbsp;&nbsp;&nbsp; 2 diluent
&nbsp;&nbsp;&nbsp; 3 guscn&nbsp; #was spare
&nbsp;&nbsp;&nbsp; 4 spare
&nbsp;&nbsp;&nbsp; 5 Sipper
&nbsp;&nbsp;&nbsp; 6 waste2
&nbsp;&nbsp;&nbsp; 7 spedil
&nbsp;&nbsp;&nbsp; 8 air clean

def diluteMFBlysate&nbsp; #apart of PRVprocess.rb
\# uses loadMFBslug above, but performs a dilution of the lysate for qPCR
\# CAN PARAMETERIZE THE DILUTION???---Comes much later. Ask Brent how...

loadMFBslug do
&nbsp; #Mixes lysate and GuSCN into syringe
&nbsp;&nbsp;&nbsp; Log.record "diluting Lysate in Syringe"
&nbsp;&nbsp;&nbsp; PSV.to :PTV
&nbsp;&nbsp;&nbsp; PTV.to :PRV
&nbsp;&nbsp;&nbsp; CBV.to :PRV
&nbsp;&nbsp;&nbsp; PRV.to :air
&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp; PRV.to CBV
&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp; PS.pull 0.1, PSslow
&nbsp;&nbsp;&nbsp; delay 5
&nbsp;&nbsp;&nbsp; PRV.to :guscn
&nbsp;&nbsp;&nbsp; PS.pull 0.9
&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp; PRV.air
&nbsp;&nbsp;&nbsp; PS.fill
&nbsp;&nbsp;&nbsp; delay 2

&nbsp; #Moves diluted lysate to PRV mixing coil
&nbsp; Log.record "Parking diluted lysate in Mixing Coil"
&nbsp;&nbsp;&nbsp; PSV.to :mixloop
&nbsp;&nbsp;&nbsp; PTV.to :PRVmixing
&nbsp;&nbsp;&nbsp; PRV.to :CBV
&nbsp;&nbsp;&nbsp; PS.push MixLoopPull&nbsp; #need to determine volume start with MixLoopPull
&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp; PSV.to waste1
&nbsp;&nbsp;&nbsp; &nbsp;PS.empty
&nbsp;&nbsp;&nbsp; &nbsp;PSV.to PTV
&nbsp;&nbsp;&nbsp; &nbsp;PTV.to PRV

&nbsp; #Rinses PRV-AIV-CBV line, bypasses mixloop
&nbsp; samplePassF

&nbsp; #Primes diluted lysate to PRV (CBV-AIV-line)
&nbsp; Log.record "moving diluted lysate into CBV-AIV line"
&nbsp;&nbsp;&nbsp; PSV.to :air
&nbsp;&nbsp;&nbsp; &nbsp;PS.fill
&nbsp;&nbsp;&nbsp; &nbsp;PSV.to :mixloop
&nbsp;&nbsp;&nbsp; &nbsp;PTV.to PRVmixing
&nbsp;&nbsp;&nbsp; &nbsp;PRV.to CBV
&nbsp;&nbsp;&nbsp; &nbsp;PS.push 0.9 PSslow
&nbsp;&nbsp;&nbsp; &nbsp;delay 2
&nbsp;&nbsp;&nbsp; &nbsp;PRV.waste2
&nbsp;&nbsp;&nbsp; &nbsp;PS.empty

&nbsp; #Mixes diluted lysate with speDil
&nbsp; Log.record "mixing lysate with speDil"
&nbsp;&nbsp;&nbsp;&nbsp; PSV.to :PML
&nbsp;&nbsp;&nbsp;&nbsp; CBV.to :PRV
&nbsp;&nbsp;&nbsp;&nbsp; PRV.to :air
&nbsp;&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp;&nbsp; PRV.to :speDil
&nbsp;&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp;&nbsp; PS.pull 0.225, PSslow
&nbsp;&nbsp;&nbsp;&nbsp; delay 5
&nbsp;&nbsp;&nbsp;&nbsp; PRV.to CBV
&nbsp;&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp;&nbsp; PS.pull .250, PSslow
&nbsp;&nbsp;&nbsp;&nbsp; delay 5
end
end

def samplePassF cleanCS = nil&nbsp; #In samplePass.rb
\#rinses PRV-AIV-CBV line, bypasses mixloop
\#run option (flush) block afterwords
\#also allows cleanCS protocol
&nbsp;Log.record "Beginning samplePassF"
&nbsp;CC.loadFlushPuck do
&nbsp;&nbsp; MFB.bypass if defined? MFB

&nbsp;&nbsp; #put 1.5ml of flush into PS
&nbsp;&nbsp; PSV.to PSR, :via=> :waste1
&nbsp;&nbsp; PSR.to :flush
&nbsp;&nbsp; PS.to 1.5
&nbsp;&nbsp; delay 5
&nbsp;&nbsp; PSV.to :waste1
&nbsp;&nbsp; PS.to 0
&nbsp;&nbsp; PSV.to PSR
&nbsp;&nbsp; PSR.to :air
&nbsp;&nbsp; PS.fill

&nbsp;&nbsp; #Backflush PRV - CBV line to CTV spit; bypasses mix loop

&nbsp;&nbsp; PRV.connect CBV
&nbsp;&nbsp; PSV.to :PTV, :via=> :air&nbsp;&nbsp; #Check this direction
&nbsp;&nbsp; CTV.to :air, :avoiding=>:intake
&nbsp;&nbsp; PTV.to :PRV
&nbsp;&nbsp; PS.to 0

&nbsp;&nbsp; #clear the line of fluid
&nbsp;&nbsp; PSV.to :air
&nbsp;&nbsp; PS.fill
&nbsp;&nbsp; PSV.to :PTV
&nbsp;&nbsp; PS.to 0
&nbsp;&nbsp; PSV.to :air
&nbsp;&nbsp; PS.fill
&nbsp;&nbsp; PSV.to :PTV
&nbsp;&nbsp;&nbsp; PS.to 0
&nbsp;&nbsp; rinseCS if cleanCS
&nbsp;&nbsp; yield if block_given?
&nbsp;end
end #samplePassF
\\]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS
\\]]></property>
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<property name="body"><![CDATA[h3.


h3. This email discusses the changes that have to occur to have HAB arrays and qPCR from one sample event.&nbsp; It also incorporates the other possible code changes that have to occur on NEO.&nbsp; We should also keep in mind running the DA arrays in concert and how this affects the plumbing and valve moves of the PRV.

\\

1.&nbsp; Copy NEO's current Flash to Tornado

{color:#3300cc}6/14/11{color}&nbsp; Tornado/ESP/NEOtombstoneCode11jun14


2.&nbsp; Update code on NEO (Brent has already updated ruby code) and determine what is now "broken"

{color:#3300cc}6/14/11{color} moved to bufflehead.&nbsp; Use user preston.&nbsp; Problems with /var/log setup and the correct path for mounting bufflehead. If it loose home or fails use /sbin/service nfsmount start to regain connection.&nbsp; You must be a superuser.&nbsp; Brent will have to look at this when he returns.&nbsp;



3.&nbsp; Rig with Dummy MFB to make seeing core moves easier
4.&nbsp; Determine if the AIV lines (to PRV and CBV) need to be changed.
&nbsp;&nbsp; &nbsp;a.&nbsp; To match other instruments and handle the larger lysate volume generated by the HAB protocol

{color:#9933cc}6/15/11{color} With the current lines on NEO and new code only recover 700ul of lysate.&nbsp; Prime is not correct we loose too much. After CS.push to 0 the line between the PRV and PTV is completely filled.&nbsp;



5.&nbsp; Do we have enough lysate volume for delivery of 1ml lysate to the array and up to 250 ul for the qPCR?
&nbsp;&nbsp; &nbsp;a.&nbsp; update PRVprocess.rb to handing the priming of the larger volume (depending on length of CBV-AIV-PRV line this may effect the positioning of the lysate to the PRV for the bacSHAmfb protocol)
6.&nbsp; Update code to deliver 1ml lysate (undiluted ) to array.&nbsp; Current protocol dilutes to 1.5M GusCN for BAC array.
7.&nbsp; Create and testing of&nbsp; habSHAmfb protocol based on the structure of the bacSHAmfb
&nbsp;&nbsp; &nbsp;a.&nbsp; Start with "normal protocol"&nbsp; 250ul of lysate and 225 ul of SPEdiluent
8.&nbsp; Testing of dilution of Lysate protocol

{color:#3300cc}6/15/11&nbsp;{color} Dilution protocol will have to include a rinse of the mixloop.&nbsp; The transferPRV protocol uses the mixloop to depressurize the lines.&nbsp; Lots of concentrated lysate.
9.&nbsp; Timing of array hybridization with lysate dilution step \--incorporation into habSHAmfb and mfb protocol
&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-----update of bacSHAmfb is not necessary for Pier deployment
10.&nbsp; CC clamp has to get the heavier springs

h3. The second email Diluting Lysate for qPCR on ESP&nbsp; (Email 2 of 2)-\- is  exactly for that lysate dilution by the core prior to delivery to the  MFB.

Brent added code to pass in an optional block in the loadMFBslug protocol, which will make its implementation much easier.&nbsp; It will have to be determined if the timing of diluting the lysate fits into the current time alloted for the hybridization of the array (if one is being run on the same sample.)&nbsp; This code starts once the concentrated lysate has been primed to the PRV.

The Major steps are:

{color:#000000}0.5&nbsp; rinse of the mixloop (Could occur prior to delivery of lysate to array.){color}


1.&nbsp; Airs out mixloop line (Currently done in loadMFBslug)
2.&nbsp; Dilution of Lysate (start with 1:10 dilution).&nbsp; Pulls lysate 0.1 ml then GuSCN 0.9ml (1ml total volume), into PS via PRV-PSV line. Then fills the syringe with air from the PRV.&nbsp; Mixes the lysate.
3.&nbsp; Move the diluted lysate into mixing coil.
4.&nbsp; Rinses the PSV-PRV-AIV/CBV line, bypasses mixloop (created samplePassF--based on samplePassCa)
5.&nbsp; Moves diluted lysate held in mixing coil to the CBV-AIV line.&nbsp; Primed to PRV.valve
6.&nbsp; Mixes diluted lysate with speDil (same protocol/ratio in loadMFBslug)
7.&nbsp; Positions slug in AIV for MFB (completes loadMFBslug)

Possible Valve Configuration Change for PRV::
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; GuSCN has to be primed to valve
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; Assumes that we don't change current DA reagent positions.

A.&nbsp; With DA reagents
&nbsp;&nbsp;&nbsp; 1 AIV/CBV
&nbsp;&nbsp;&nbsp; 2 ab1
&nbsp;&nbsp;&nbsp; 3 speDil
&nbsp;&nbsp;&nbsp; 4 guscn
&nbsp;&nbsp;&nbsp; 5 Sipper // diluent?
&nbsp;&nbsp;&nbsp; 6 waste2
&nbsp;&nbsp;&nbsp; 7 ab2
&nbsp;&nbsp;&nbsp; 8 air clean
If BAC arrays are performed on samples also for qPCR, then the sipper has to be converted into diluent.

B.&nbsp; w/o DA reagents&nbsp; (Nearly same as current PRV valve with MFB attached)
&nbsp;&nbsp;&nbsp; 1 AIV/CBV
&nbsp;&nbsp;&nbsp; 2 diluent
&nbsp;&nbsp;&nbsp; 3 guscn&nbsp; #was spare
&nbsp;&nbsp;&nbsp; 4 spare
&nbsp;&nbsp;&nbsp; 5 Sipper
&nbsp;&nbsp;&nbsp; 6 waste2
&nbsp;&nbsp;&nbsp; 7 spedil
&nbsp;&nbsp;&nbsp; 8 air clean

def diluteMFBlysate&nbsp; #apart of PRVprocess.rb
\# uses loadMFBslug above, but performs a dilution of the lysate for qPCR
\# CAN PARAMETERIZE THE DILUTION???---Comes much later. Ask Brent how...

loadMFBslug do
&nbsp; #Mixes lysate and GuSCN into syringe
&nbsp;&nbsp;&nbsp; Log.record "diluting Lysate in Syringe"
&nbsp;&nbsp;&nbsp; PSV.to :PTV
&nbsp;&nbsp;&nbsp; PTV.to :PRV
&nbsp;&nbsp;&nbsp; CBV.to :PRV
&nbsp;&nbsp;&nbsp; PRV.to :air
&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp; PRV.to CBV
&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp; PS.pull 0.1, PSslow
&nbsp;&nbsp;&nbsp; delay 5
&nbsp;&nbsp;&nbsp; PRV.to :guscn
&nbsp;&nbsp;&nbsp; PS.pull 0.9
&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp; PRV.air
&nbsp;&nbsp;&nbsp; PS.fill
&nbsp;&nbsp;&nbsp; delay 2

&nbsp; #Moves diluted lysate to PRV mixing coil
&nbsp; Log.record "Parking diluted lysate in Mixing Coil"
&nbsp;&nbsp;&nbsp; PSV.to :mixloop
&nbsp;&nbsp;&nbsp; PTV.to :PRVmixing
&nbsp;&nbsp;&nbsp; PRV.to :CBV
&nbsp;&nbsp;&nbsp; PS.push MixLoopPull&nbsp; #need to determine volume start with MixLoopPull
&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp; PSV.to waste1
&nbsp;&nbsp;&nbsp; &nbsp;PS.empty
&nbsp;&nbsp;&nbsp; &nbsp;PSV.to PTV
&nbsp;&nbsp;&nbsp; &nbsp;PTV.to PRV

&nbsp; #Rinses PRV-AIV-CBV line, bypasses mixloop
&nbsp; samplePassF

&nbsp; #Primes diluted lysate to PRV (CBV-AIV-line)
&nbsp; Log.record "moving diluted lysate into CBV-AIV line"
&nbsp;&nbsp;&nbsp; PSV.to :air
&nbsp;&nbsp;&nbsp; &nbsp;PS.fill
&nbsp;&nbsp;&nbsp; &nbsp;PSV.to :mixloop
&nbsp;&nbsp;&nbsp; &nbsp;PTV.to PRVmixing
&nbsp;&nbsp;&nbsp; &nbsp;PRV.to CBV
&nbsp;&nbsp;&nbsp; &nbsp;PS.push 0.9 PSslow
&nbsp;&nbsp;&nbsp; &nbsp;delay 2
&nbsp;&nbsp;&nbsp; &nbsp;PRV.waste2
&nbsp;&nbsp;&nbsp; &nbsp;PS.empty

&nbsp; #Mixes diluted lysate with speDil
&nbsp; Log.record "mixing lysate with speDil"
&nbsp;&nbsp;&nbsp;&nbsp; PSV.to :PML
&nbsp;&nbsp;&nbsp;&nbsp; CBV.to :PRV
&nbsp;&nbsp;&nbsp;&nbsp; PRV.to :air
&nbsp;&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp;&nbsp; PRV.to :speDil
&nbsp;&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp;&nbsp; PS.pull 0.225, PSslow
&nbsp;&nbsp;&nbsp;&nbsp; delay 5
&nbsp;&nbsp;&nbsp;&nbsp; PRV.to CBV
&nbsp;&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp;&nbsp; PS.pull .250, PSslow
&nbsp;&nbsp;&nbsp;&nbsp; delay 5
end
end

def samplePassF cleanCS = nil&nbsp; #In samplePass.rb
\#rinses PRV-AIV-CBV line, bypasses mixloop
\#run option (flush) block afterwords
\#also allows cleanCS protocol
&nbsp;Log.record "Beginning samplePassF"
&nbsp;CC.loadFlushPuck do
&nbsp;&nbsp; MFB.bypass if defined? MFB

&nbsp;&nbsp; #put 1.5ml of flush into PS
&nbsp;&nbsp; PSV.to PSR, :via=> :waste1
&nbsp;&nbsp; PSR.to :flush
&nbsp;&nbsp; PS.to 1.5
&nbsp;&nbsp; delay 5
&nbsp;&nbsp; PSV.to :waste1
&nbsp;&nbsp; PS.to 0
&nbsp;&nbsp; PSV.to PSR
&nbsp;&nbsp; PSR.to :air
&nbsp;&nbsp; PS.fill

&nbsp;&nbsp; #Backflush PRV - CBV line to CTV spit; bypasses mix loop

&nbsp;&nbsp; PRV.connect CBV
&nbsp;&nbsp; PSV.to :PTV, :via=> :air&nbsp;&nbsp; #Check this direction
&nbsp;&nbsp; CTV.to :air, :avoiding=>:intake
&nbsp;&nbsp; PTV.to :PRV
&nbsp;&nbsp; PS.to 0

&nbsp;&nbsp; #clear the line of fluid
&nbsp;&nbsp; PSV.to :air
&nbsp;&nbsp; PS.fill
&nbsp;&nbsp; PSV.to :PTV
&nbsp;&nbsp; PS.to 0
&nbsp;&nbsp; PSV.to :air
&nbsp;&nbsp; PS.fill
&nbsp;&nbsp; PSV.to :PTV
&nbsp;&nbsp;&nbsp; PS.to 0
&nbsp;&nbsp; rinseCS if cleanCS
&nbsp;&nbsp; yield if block_given?
&nbsp;end
end #samplePassF\\]]></property>
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<property name="body"><![CDATA[h3.


h3. This email discusses the changes that have to occur to have HAB arrays and qPCR from one sample event.&nbsp; It also incorporates the other possible code changes that have to occur on NEO.&nbsp; We should also keep in mind running the DA arrays in concert and how this affects the plumbing and valve moves of the PRV.
\\

1.&nbsp; Copy NEO's current Flash to Tornado
2.&nbsp; Update code on NEO (Brent has already updated ruby code) and determine what is now "broken"
3.&nbsp; Rig with Dummy MFB to make seeing core moves easier
4.&nbsp; Determine if the AIV lines (to PRV and CBV) need to be changed.
&nbsp;&nbsp; &nbsp;a.&nbsp; To match other instruments and handle the larger lysate volume generated by the HAB protocol
5.&nbsp; Do we have enough lysate volume for delivery of 1ml lysate to the array and up to 250 ul for the qPCR?
&nbsp;&nbsp; &nbsp;a.&nbsp; update PRVprocess.rb to handing the priming of the larger volume (depending on length of CBV-AIV-PRV line this may effect &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;the positioning of the lysate to the PRV for the bacSHAmfb protocol)
6.&nbsp; Update code to deliver 1ml lysate (undiluted ) to array.&nbsp; Current protocol dilutes to 1.5M GusCN for BAC array.
7.&nbsp; Create and testing of&nbsp; habSHAmfb protocol based on the structure of the bacSHAmfb
&nbsp;&nbsp; &nbsp;a.&nbsp; Start with "normal protocol"&nbsp; 250ul of lysate and 225 ul of SPEdiluent
8.&nbsp; Testing of dilution of Lysate protocol
9.&nbsp; Timing of array hybridization with lysate dilution step \--incorporation into habSHAmfb and mfb protocol
&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-----update of bacSHAmfb is not necessary for Pier deployment
10.&nbsp; CC clamp has to get the heavier springs


h3. The second email Diluting Lysate for qPCR on ESP&nbsp; (Email 2 of 2)-\- is  exactly for that lysate dilution by the core prior to delivery to the  MFB.

Brent added code to pass in an optional block in the loadMFBslug protocol, which will make its implementation much easier.&nbsp; It will have to be determined if the timing of diluting the lysate fits into the current time alloted for the hybridization of the array (if one is being run on the same sample.)&nbsp; This code starts once the concentrated lysate has been primed to the PRV.

The Major steps are:

1.&nbsp; Airs out mixloop line (Currently done in loadMFBslug)
2.&nbsp; Dilution of Lysate (start with 1:10 dilution).&nbsp; Pulls lysate 0.1 ml then GuSCN 0.9ml (1ml total volume), into PS via PRV-PSV line. Then fills the syringe with air from the PRV.&nbsp; Mixes the lysate.
3.&nbsp; Move the diluted lysate into mixing coil.
4.&nbsp; Rinses the PSV-PRV-AIV/CBV line, bypasses mixloop (created samplePassF--based on samplePassCa)
5.&nbsp; Moves diluted lysate held in mixing coil to the CBV-AIV line.&nbsp; Primed to PRV.valve
6.&nbsp; Mixes diluted lysate with speDil (same protocol/ratio in loadMFBslug)
7.&nbsp; Positions slug in AIV for MFB (completes loadMFBslug)


Possible Valve Configuration Change for PRV::
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; GuSCN has to be primed to valve
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; Assumes that we don't change current DA reagent positions.

A.&nbsp; With DA reagents
&nbsp;&nbsp;&nbsp; 1 AIV/CBV
&nbsp;&nbsp;&nbsp; 2 ab1
&nbsp;&nbsp;&nbsp; 3 speDil
&nbsp;&nbsp;&nbsp; 4 guscn
&nbsp;&nbsp;&nbsp; 5 Sipper // diluent?
&nbsp;&nbsp;&nbsp; 6 waste2
&nbsp;&nbsp;&nbsp; 7 ab2
&nbsp;&nbsp;&nbsp; 8 air clean
If BAC arrays are performed on samples also for qPCR, then the sipper has to be converted into diluent.



B.&nbsp; w/o DA reagents&nbsp; (Nearly same as current PRV valve with MFB attached)
&nbsp;&nbsp;&nbsp; 1 AIV/CBV
&nbsp;&nbsp;&nbsp; 2 diluent
&nbsp;&nbsp;&nbsp; 3 guscn&nbsp; #was spare
&nbsp;&nbsp;&nbsp; 4 spare
&nbsp;&nbsp;&nbsp; 5 Sipper
&nbsp;&nbsp;&nbsp; 6 waste2
&nbsp;&nbsp;&nbsp; 7 spedil
&nbsp;&nbsp;&nbsp; 8 air clean

def diluteMFBlysate&nbsp; #apart of PRVprocess.rb
\# uses loadMFBslug above, but performs a dilution of the lysate for qPCR
\# CAN PARAMETERIZE THE DILUTION???---Comes much later. Ask Brent how...

loadMFBslug do
&nbsp; #Mixes lysate and GuSCN into syringe
&nbsp;&nbsp;&nbsp; Log.record "diluting Lysate in Syringe"
&nbsp;&nbsp;&nbsp; PSV.to :PTV
&nbsp;&nbsp;&nbsp; PTV.to :PRV
&nbsp;&nbsp;&nbsp; CBV.to :PRV
&nbsp;&nbsp;&nbsp; PRV.to :air
&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp; PRV.to CBV
&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp; PS.pull 0.1, PSslow
&nbsp;&nbsp;&nbsp; delay 5
&nbsp;&nbsp;&nbsp; PRV.to :guscn
&nbsp;&nbsp;&nbsp; PS.pull 0.9
&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp; PRV.air
&nbsp;&nbsp;&nbsp; PS.fill
&nbsp;&nbsp;&nbsp; delay 2

&nbsp; #Moves diluted lysate to PRV mixing coil
&nbsp; Log.record "Parking diluted lysate in Mixing Coil"
&nbsp;&nbsp;&nbsp; PSV.to :mixloop
&nbsp;&nbsp;&nbsp; PTV.to :PRVmixing
&nbsp;&nbsp;&nbsp; PRV.to :CBV
&nbsp;&nbsp;&nbsp; PS.push MixLoopPull&nbsp; #need to determine volume start with MixLoopPull
&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp; PSV.to waste1
&nbsp;&nbsp;&nbsp; &nbsp;PS.empty
&nbsp;&nbsp;&nbsp; &nbsp;PSV.to PTV
&nbsp;&nbsp;&nbsp; &nbsp;PTV.to PRV

&nbsp; #Rinses PRV-AIV-CBV line, bypasses mixloop
&nbsp; samplePassF

&nbsp; #Primes diluted lysate to PRV (CBV-AIV-line)
&nbsp; Log.record "moving diluted lysate into CBV-AIV line"
&nbsp;&nbsp;&nbsp; PSV.to :air
&nbsp;&nbsp;&nbsp; &nbsp;PS.fill
&nbsp;&nbsp;&nbsp; &nbsp;PSV.to :mixloop
&nbsp;&nbsp;&nbsp; &nbsp;PTV.to PRVmixing
&nbsp;&nbsp;&nbsp; &nbsp;PRV.to CBV
&nbsp;&nbsp;&nbsp; &nbsp;PS.push 0.9 PSslow
&nbsp;&nbsp;&nbsp; &nbsp;delay 2
&nbsp;&nbsp;&nbsp; &nbsp;PRV.waste2
&nbsp;&nbsp;&nbsp; &nbsp;PS.empty

&nbsp; #Mixes diluted lysate with speDil
&nbsp; Log.record "mixing lysate with speDil"
&nbsp;&nbsp;&nbsp;&nbsp; PSV.to :PML
&nbsp;&nbsp;&nbsp;&nbsp; CBV.to :PRV
&nbsp;&nbsp;&nbsp;&nbsp; PRV.to :air
&nbsp;&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp;&nbsp; PRV.to :speDil
&nbsp;&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp;&nbsp; PS.pull 0.225, PSslow
&nbsp;&nbsp;&nbsp;&nbsp; delay 5
&nbsp;&nbsp;&nbsp;&nbsp; PRV.to CBV
&nbsp;&nbsp;&nbsp;&nbsp; delay 2
&nbsp;&nbsp;&nbsp;&nbsp; PS.pull .250, PSslow
&nbsp;&nbsp;&nbsp;&nbsp; delay 5
end
end

def samplePassF cleanCS = nil&nbsp; #In samplePass.rb
\#rinses PRV-AIV-CBV line, bypasses mixloop
\#run option (flush) block afterwords
\#also allows cleanCS protocol
&nbsp;Log.record "Beginning samplePassF"
&nbsp;CC.loadFlushPuck do
&nbsp;&nbsp; MFB.bypass if defined? MFB

&nbsp;&nbsp; #put 1.5ml of flush into PS
&nbsp;&nbsp; PSV.to PSR, :via=> :waste1
&nbsp;&nbsp; PSR.to :flush
&nbsp;&nbsp; PS.to 1.5
&nbsp;&nbsp; delay 5
&nbsp;&nbsp; PSV.to :waste1
&nbsp;&nbsp; PS.to 0
&nbsp;&nbsp; PSV.to PSR
&nbsp;&nbsp; PSR.to :air
&nbsp;&nbsp; PS.fill

&nbsp;&nbsp; #Backflush PRV - CBV line to CTV spit; bypasses mix loop

&nbsp;&nbsp; PRV.connect CBV
&nbsp;&nbsp; PSV.to :PTV, :via=> :air&nbsp;&nbsp; #Check this direction
&nbsp;&nbsp; CTV.to :air, :avoiding=>:intake
&nbsp;&nbsp; PTV.to :PRV
&nbsp;&nbsp; PS.to 0

&nbsp;&nbsp; #clear the line of fluid
&nbsp;&nbsp; PSV.to :air
&nbsp;&nbsp; PS.fill
&nbsp;&nbsp; PSV.to :PTV
&nbsp;&nbsp; PS.to 0
&nbsp;&nbsp; PSV.to :air
&nbsp;&nbsp; PS.fill
&nbsp;&nbsp; PSV.to :PTV
&nbsp;&nbsp;&nbsp; PS.to 0
&nbsp;&nbsp; rinseCS if cleanCS
&nbsp;&nbsp; yield if block_given?
&nbsp;end
end #samplePassF



&nbsp;]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]
# [Apr 12] \-\- Roman at WHOI, Chris P Europe
# Apr 19
# [Apr 26]
# [May 10]
# [May 17]
# May 24 \-\- Roman at WHOI, Chris S at WHOI, Chris P out
# [Jun 14]]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]
# [Apr 12] \-\- Roman at WHOI, Chris P Europe
# Apr 19
# [Apr 26]
# [May 10]
# [May 17]
# May 24 \-\- Roman at WHOI, Chris S at WHOI, Chris P out
# [Jun 14] \-- This has link to lysate dilution page]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Bill, Elif, Chris P, Julie, Jim, Roman

h3. &nbsp;Items:

&nbsp;1.&nbsp; JdF
* Ball had to be reopened to switch a communications pin.&nbsp; Will use this time to reload some testing pucks.&nbsp; Will not change PCR reagents.&nbsp; Will re-seal later today.&nbsp;
* Doug planning on test tank Weds.

2.&nbsp; Drifter
* Julie working on MFB 1.&nbsp; Her assays have been qualified on another MFB, so currently concentrating on being able to filter 2L, and what this does to the SPE efficiency, etc.&nbsp; Should be getting Hawaii water end of this week.&nbsp; Will test with that and higher-pressure pressure pots. &nbsp;

# Doug has found ground fault b/w ball and frame (reads 2 ohms).&nbsp; Mitigate by lots of zincs and short deployment time (10 days).
# Carousel issues.&nbsp; Motor drawing far too much current and hot.&nbsp;  Lubed carousel, loosened motor belt, milled home flag so no drag.&nbsp;  Better, but still not like Moe.&nbsp; Decided to go with it.
# ISUS is two week late.&nbsp; Unable to test new cable from (new) pressure housing to ball, as we needed to close the sphere.
# Harvard's PCR ass]]></property>
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<property name="version">4</property>
<property name="creatorName"><![CDATA[brent]]></property>
<property name="creationDate">2009-10-07 16:33:59.357</property>
<property name="lastModifierName"><![CDATA[brent]]></property>
<property name="lastModificationDate">2009-10-07 16:45:45.620</property>
<property name="versionComment"><![CDATA[]]></property>
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<property name="version">3</property>
<property name="creatorName"><![CDATA[brent]]></property>
<property name="creationDate">2009-10-07 16:33:59.357</property>
<property name="lastModifierName"><![CDATA[brent]]></property>
<property name="lastModificationDate">2009-10-07 16:36:31.170</property>
<property name="versionComment"><![CDATA[]]></property>
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<property name="body"><![CDATA[# [4K Sphere]]]></property>
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<property name="body"><![CDATA[h5. Goal

This meeting is to give an update and a walk through of the ESP GUI components, to get feedback and to put out a list of requests for things moving forward.

h5. Attendees

* Kevin Gomes
* Rich Schramm
* Brian Schlining

h5. Agenda

# Walk through of Planning/DM GUI
## [Deployment Diagram|ESPAPP:Design]
## [Starting the GUI|ESPAPP:2G ESP GUI Application]
## Setting preferences (Directory is local, repo is shared)
## Create new Instrument
## Create new deployment
# Walk through Dashboard
## Show work to date
### Use feedback (split and view)
## Talk about [Dashboard data protocol|ESPAPP:Real-Time ESP state update protocol framework]
# Walk through of Image Analysis
## Demo
## Show [wiki page|ESPAPP:ESP Image Analysis Application] for use
## Matlab

h5. Open issues

# Plan/Data
## Need way to determine exactly which contextual sensors on on ESP (CTD, ISUS, etc.)
## Need something in the log file that indicates when a DWSM inhale is done
# Dashboard
## Need to get data/simulator to start driving dashboard for development
## How do we then take this protocol and persist for playback (i.e. log file entries?)
# Image Analysis
## Got what he needs to keep going.

h5. Suggestions

# PCR Plots need separate axes for Temp and diode data.]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]]]></property>
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<property name="body"><![CDATA[h5. Goal

This meeting is to give an update and a walk through of the ESP GUI components, to get feedback and to put out a list of requests for things moving forward.

h5. Attendees

* Kevin Gomes
* Rich Schramm
* Brian Schlining

h5. Agenda

# Walk through of Planning/DM GUI
## [Deployment Diagram|ESPAPP:Design]
## [Starting the GUI|ESPAPP:2G ESP GUI Application]
## Setting preferences (Directory is local, repo is shared)
## Create new Instrument
## Create new deployment
# Walk through Dashboard
## Show work to date
### Use feedback (split and view)
## Talk about [Dashboard data protocol|ESPAPP:Real-Time ESP state update protocol framework]
# Walk through of Image Analysis
## Demo
## Show [wiki page|ESPAPP:ESP Image Analysis Application] for use
## Matlab

h5. Open issues

# Plan/Data
## Need way to determine exactly which contextual sensors on on ESP (CTD, ISUS, etc.)
## Need something in the log file that indicates when a DWSM inhale is done
# Dashboard
## Need to get data/simulator to start driving dashboard for development
## How do we then take this protocol and persist for playback (i.e. log file entries?)
# Image Analysis
## Got what he needs to keep going.

h5. Suggestions

# PCR Plots need separate axes for Temp and diode data.
# After adding assay, planned table does not updage]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris S., Jim, Brent, Doug, Wayne, Scott, Cheri
Absent:&nbsp;&nbsp; Addie (maternity)

h3. Machine Builds

* &nbsp;Feb 23 Cheri finishes core builds and calibrations
* New battery connectors for surface-can lids have been ordered.

h3. MFB

* &nbsp;Cheri will ship 3 MFB kits to McLane tomorrow.&nbsp; Chris S. will cut PO to pay for assembly of 2 of them.&nbsp; Kits will not have instructions included.&nbsp; Tim can get copies of things when he's out next week for core assembly
* USCS people now finished with MFB01 and we can proceed with integration on MOE.&nbsp; Will do it the week of Feb 17; next week Scott will work on single connector, week after that Cheri can do mechanical merging.

h3. Software

* &nbsp;Ruby patch on all machines except MFB02, MFB03, Gordon, and Betty.
* Brent needs more cables:
** serial & debug cable (10-pin to DB9)
** PCR w/ level-shifter
** J-TAG cables
* Discussion about the need for more (newer?) laptops.&nbsp; Brent and Jim will talk to Todd.
* McLane needs one laptop that runs LINUS.&nbsp; (this typo purposely inserted to see who reads these notes).&nbsp; Again, will talk to Todd about getting a machine.
* Checksum difference--Wayne DID get correct bits eventually, so gave to DWSM and seems to be working.
* Wayne, Brent, Scott, Doug to meet at 10am tomorrow to discuss DWSM issues
* Wayne thinks 1 more day on dPress stuff and hardware

h3. DWSM


h6. +Sphere+

Sphere is approved to 4000m\!&nbsp; Hooray.
\\

h6. +Elevator+

* &nbsp;CRP may be moving up their foam delivery date to mid-March due to some prior order cancellations
* It will need machining; still to determine who will do that
* Modem;&nbsp; we only have USBL transducers on the ships, but not lots of track record with this modem for both communications and release.&nbsp; Brent will talk to Dale Graves about this to help us decide what to go with.
* Although it's a back-burner issue, Doug will check with Flyer winch specs to see if it would be possible to use Spectra line to help place the D-ESP.

*{+}DWSM{+}*
* &nbsp;SeaConn will deliver elevator cable MARCH 13
* for wet-mate connector, we will use FOCE spare ODI connector--terminate exactly same way as on FOCE.
* Question as to whether the SIM-Can will go with us on the Northern Expedition.
* One pump on DWSM seems bad; Doug looking into getting replacement
* Brent will start working on DWSM control next week, after latest firmware on all dwarves.

h3. Other Items:

* &nbsp;]]></property>
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<property name="body"><![CDATA[h5. Goal

This meeting is to give an update and a walk through of the ESP GUI components, to get feedback and to put out a list of requests for things moving forward.

h5. Attendees

* Kevin Gomes
* Rich Schramm
* Brian Schlining

h5. Agenda

* Walk through of Planning/DM GUI
** 
* Walk through of Image Analysis

h5. Open issues

# Need something in the log file that indicates when a DWSM inhale is done
]]></property>
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<property name="body"><![CDATA[Our first 'labeled' scintered frits arrived 23 April, 2008.&nbsp; These were 10um frits, labeled 'D'. Specifics of this order:

Job #36366
Disc Dimensions: 0.998 \+0.000/-0.002" OD x 0.062 \+/-0.005" thick
Porous Grade: 10 Micron Grade
No Chamfers
Porous material Chemistry: Titanium Grade 2 per unified
PO# 0810358&nbsp;

These frits did {color:#cc0000}NOT{color} have finished edges, and were 0.057" in thickness, within tolerance specified, but thinner than original frits.
Future orders should specify edging and a lower thickness tolerance to get closer to the 0.062" thickness.\\

The convention, decided in emails Feb 26, 2008, will be:

0.1, 0.5, 1, 10um frits will be labeled

A, B, C, D respectively.&nbsp;
\\

We have had CE Metallurgical make the 'press' for these so subsequent batches should be less expensive.&nbsp;
\\

{color:#0000ff}Contact{color}:

Chand Eisenmann Metallurgical
258 Spielman Hwy
Burlington, CT&nbsp; 06013

860-675-5000

{color:#0000ff}email:{color}
me@chandeisenmann.com&nbsp; (Mark)]]></property>
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<property name="body"><![CDATA[h5. Goal

This meeting is to give an update and a walk through of the ESP GUI components, to get feedback and to put out a list of requests for things moving forward.

h5. Attendees

* Kevin Gomes
* Rich Schramm
* Brian Schlining

h5. Agenda

# Walk through of Planning/DM GUI
## [Deployment Diagram|ESPAPP:Design]
## [Starting the GUI|ESPAPP:2G ESP GUI Application]
## Setting preferences (Directory is local, repo is shared)
## Create new Instrument
## Create new deployment
# Walk through of Image Analysis

h5. Open issues

# Need way to determine exactly which contextual sensors on on ESP (CTD, ISUS, etc.)
# Need something in the log file that indicates when a DWSM inhale is done

h5. Suggestions

# PCR Plots need separate axes for Temp and diode data.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim B., Chris P, Roman M., Wayne R., Cheri E., Brent R., Julie R., Scott J.

Absent:&nbsp; Chris Scholin, Doug Pargett.\\ \\]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
\\
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage taken by Rob Vincent:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]

Map of locations:&nbsp; [http://maps.google.com/maps/ms?ie=UTF&msa=0&msid=213220825771739778963.0004a40bdd601babc291d]

May 23.&nbsp; Attempted recovery of ESP.&nbsp; Message from Roman:

{color:#996600}&nbsp;&nbsp;&nbsp; We went out to the site where espbruce was moored and attempted to find it.&nbsp; The weather was very poor and water was very turbid.&nbsp; Using the ships depth finder we found a promising target.&nbsp; In difficult conditions the divers performed a search but espbruce was not found.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; We recovered the mooring.&nbsp; It looks like the cable was pulled straight out of the cone.&nbsp; The top mast is bent but I cannot say if this was caused by a rough landing on the beach or boat impact.&nbsp; There are no dents or gouges on the mooring.&nbsp; The radio box is dry and antenna looks ok.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; Thursday the RV Gulf Challenger may be able to survey the area with a side scanning sonar.&nbsp; This will be a much better way to search for espbruce.&nbsp;{color}

Message from Roman May 26:

{color:#996600}&nbsp;&nbsp;&nbsp; ESPbruce was located at&nbsp; 43° 02.0740 N&nbsp;&nbsp; 70° 36.8447 W at ~ 10m depth.&nbsp; This position is about 19 yards from the waypoint.&nbsp; So looks like it wasn't dragged and has maintained seal integrity.&nbsp; We will attempt to recover it this weekend if we can get the RV Tioga.&nbsp; If not will recover with the RV Connecticut on june 7th weather permitting.{color}
&nbsp;

Dates for a recovery kept moving as weather and scheduling problems arose.&nbsp; Finally, Roman reported on June 15:
{quote}\\
{quote}
&nbsp;{color:#996600}&nbsp;&nbsp; ESPbruce was recovered today with no visible external damage. The EM cable strain relief is still on the cable.&nbsp; The recovery operation used two ships the RV Gulf Challenger and it's sister the RV Tioga.&nbsp; The Challenger supported the the side scan survey and the Tioga supported the divers and lifting of the core package and its anchor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;The side scan sonar operator advised me at the beginning of the day that he believed the esp package would be found on the bottom.&nbsp; He based this opinion on the data secured by his colleague almost two weeks ago.&nbsp; From his read of that run, he believed that the instrument was 15m off the bottom at that time.&nbsp; Depth at this site is 49m.&nbsp; He felt that the instrument was slowly sinking and that by today it was surly be on the sea floor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Todays side scan survey took approximately 90 minutes.&nbsp; They had acquired a strong signature on the core and calculated that it was at a depth of 65 feet (~20m). The package&nbsp; was still located within 10m of the original deployment site.&nbsp; They dropped a marker line with a float as close to the calculated position as possible.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;At this point divers equipped with twin 80 cu ft Nitrox cylinders and electric scooters dived on the marker.&nbsp; They had 70 minutes of search time.&nbsp; After 42 minutes an orange sausage float attached to a spectra lift line appeared.&nbsp; Then 10 minutes later a second lift bag attached to the EM cable appeared.&nbsp; The divers surfaced after a total bottom time of 62 minutes.&nbsp; Eight minutes to spare.&nbsp; We recovered the divers.&nbsp; They reported that the depth of top of the can was at 26 feet (~8m) right where it was supposed to be.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Recovery went smoothly using a single winch equipped with a capstan attachment.&nbsp; By alternately shifting the load from drum (used to lift anchor) and capstan (used to lift instrument we recovered the package and the anchor safely.{color}
{quote}
\\ \\  {color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford.
\\]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.\\
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage taken by Rob Vincent:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]

Map of locations:&nbsp; [http://maps.google.com/maps/ms?ie=UTF&msa=0&msid=213220825771739778963.0004a40bdd601babc291d]

May 23.&nbsp; Attempted recovery of ESP.&nbsp; Message from Roman:

{color:#996600}&nbsp;&nbsp;&nbsp; We went out to the site where espbruce was moored and attempted to find it.&nbsp; The weather was very poor and water was very turbid.&nbsp; Using the ships depth finder we found a promising target.&nbsp; In difficult conditions the divers performed a search but espbruce was not found.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; We recovered the mooring.&nbsp; It looks like the cable was pulled straight out of the cone.&nbsp; The top mast is bent but I cannot say if this was caused by a rough landing on the beach or boat impact.&nbsp; There are no dents or gouges on the mooring.&nbsp; The radio box is dry and antenna looks ok.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; Thursday the RV Gulf Challenger may be able to survey the area with a side scanning sonar.&nbsp; This will be a much better way to search for espbruce.&nbsp;{color}

Message from Roman May 26:

{color:#996600}&nbsp;&nbsp;&nbsp; ESPbruce was located at&nbsp; 43° 02.0740 N&nbsp;&nbsp; 70° 36.8447 W at ~ 10m depth.&nbsp; This position is about 19 yards from the waypoint.&nbsp; So looks like it wasn't dragged and has maintained seal integrity.&nbsp; We will attempt to recover it this weekend if we can get the RV Tioga.&nbsp; If not will recover with the RV Connecticut on june 7th weather permitting.{color}
&nbsp;
{quote}\\
\\
\\
\\

{color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford. ]]></property>
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process.

h3. Requirements
|| Number || Requirement || Goal ||
| | User can define missions by specifying phases | Planning |
| | User can specify and adjust phase start times | Planning |
| | User can also specify a time to wait between events instead of a specific start time | Planning |
| | User can set mission start and end times that are not associated with a phase/protocol | Planning |
| | User can specify comments associated with missions that are printed at the top of the mission script | Planning |
| | After planning, application should generate mission script, puck loads, and reagent volumes | Planning |
| | User can add comments to a phase that will be generated in the script | Planning |
| | Users can add/delete/edit protocol runs and phases | Planning |
| | Users can add/delete/edit consumables | Planning |
| | Users can schedule Kills (end purges) or disable kills | Planning |
| | Users can define generic events and what script will actually be added to the master script (if needed) | Planning |
| | Mission plan generation will include a puck loading list | Planning |
| | User can associate external files with events (excel spreadsheet, documents, etc.) | Planning, Data Management |
| | Tide and phase information will be available | Planning, Data Management |
| | Application will list sample volumes with protocol run | Planning, Data Management |
| | User can add non-phase/protocol events (user defined) to the calendar anywhere | Data Management |
| | User can view images associated with phases | Data Management |
| | User can browse the .GAL file along with image and filter paper information | Data Management |
| | User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density | Data Management |
| | User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery | Data Management |
| | When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown | Data Management |
| | Application should allow for details of flushes to be seen/accounted for | Data Management |
| | The application should archive (and make available) the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts | Data Management |
| | Users should be able to download instrument logs and images and the GUI will parse out the following events:
* Track deployments of contextual sensors (sub-deployments of ESP)
* Collection of contextual sensor data (with capability to view/work with data) 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time | Data Management, State Visualization |
| | Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power | State Visualization |
| | Users can visualize the current state of the instrument | State Visualization |
| | Users can scroll back in time and visualize instrument state at the various points in time | State Visualization |

h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Glossary]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
{panel}
{column}
{section}
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<property name="body"><![CDATA[Present:&nbsp; Jim, Chris P, Elif, Roman


h4. Items:

# Cold testing for WHOI deployment.
## Elif has compared old wash buffer with 'modified' wash (50% wash, 50% buffer E) (at 2 degrees, viscosity of wash \~10, modified wash \~3)
### blocking effciency on blank filter is similar
### signal with biomaterial similar (BAC arrays)
### moving to test HAB culture; if no difference, then moving to run HAB culture in cold.
### ESP-Bruce going into cold on Thursday.
# Array printing
## Roman planning a massive, 1-week printing run in early Feb.&nbsp; Will try and knock out all WHOI arrays.

3.  Discussion about using an unbuilt MFB for G3 development.&nbsp; Each missing some parts.&nbsp; Must talk to Chris P before building to know what needs to be done.
\\

Discussion of schedule, both for WHOI deployment and JdeFuca in July. \\

Machine Plans:

&nbsp;Gordon \-\- D-ESP

Betty \-\- still to be finished; plan is June/July

Moe \-\- Spring deployment at M0 and Drifter in Fall

Mack & NEO-\- Fall Biospace deployemtn

Bruce \-\- WHOI spring deployemtn
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<property name="body"><![CDATA[Present:&nbsp; Jim, Chris P, Chris S., Elif, Roman, Bill U.

h4. Items:

# Cold testing for WHOI deployment.
## Elif has compared old wash buffer with 'modified' wash (50% wash, 50% buffer E) (at 2 degrees, viscosity of wash \~10, modified wash \~3)
### blocking effciency on blank filter is similar
### signal with biomaterial similar (BAC arrays)
### moving to test HAB culture; if no difference, then moving to run HAB culture in cold.
### ESP-Bruce going into cold on Thursday.
# Array printing
## Roman planning a massive, 1-week printing run in early Feb.&nbsp; Will try and knock out all WHOI arrays.

3.  Discussion about using an unbuilt MFB for G3 development.&nbsp; Each missing some parts.&nbsp; Must talk to Chris P before building to know what needs to be done.\\

Discussion of schedule, both for WHOI deployment and JdeFuca in July. ]]></property>
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<property name="body"><![CDATA[h3. Machine Builds

* G

h3. MFB


h3.

* &nbsp;

h3. Drifter

* Gements.

h3. Software

* &nbsp;Bitive.

h3. Deep ESP


h6. +Sphere+

* Pas

h6. +Elevator+

* el bldg D.

*{+}DWSM{+}*
* Sw
** ed.

h3. GUI

* &nbsp;Br.

h3. Deployment Issues

* &nbsp;AprK (with new lo

h3. Other Items:

* &nbsp;VJulie ae gone]]></property>
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<property name="body"><![CDATA[h5. Goal

This meeting is to give an update and a walk through of the ESP GUI components, to get feedback and to put out a list of requests for things moving forward.

h5. Attendees

* Kevin Gomes
* Rich Schramm
* Brian Schlining

h5. Agenda

* Walk through of Planning/DM GUI
* Walk through of Image Analysis

h5. Open issues

# Need something in the log file that indicates when a DWSM inhale is done
]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] \- first discussion of adaptive sampling strategies
# Mar 3 - CMORE Hawaii
# [Mar 10] \-\- wand schematic
# [Mar 17]
# [Mar 24]
# Mar 31 - team deploying MOE at M0; Brent at WHOI
# [Apr 7]
# [Apr 14]
# [Apr 21]\--wand schematic reminder...
# [Apr 28]\--D-ESP 2-Year Birthday Celebration\!\!&nbsp; (Poster is [here|^ESP Birthday Poster(smaller).pdf])
# May 5 \-\- Visit to ASU
# [May 12]
# [May 19]
# [May 26]
# [Jun 2]]]></property>
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process.

h3. Requirements
|| Number || Requirement || Goal ||
| | User can define missions by specifying phases | Planning |
| | User can specify and adjust phase start times | Planning |
| | User can also specify a time to wait between events instead of a specific start time | Planning |
| | User can set mission start and end times that are not associated with a phase/protocol | Planning |
| | User can specify comments associated with missions that are printed at the top of the mission script | Planning |
| | After planning, application should generate mission script, puck loads, and reagent volumes | Planning |
| | User can add comments to a phase that will be generated in the script | Planning |
| | Users can add/delete/edit protocol runs and phases | Planning |
| | Users can add/delete/edit consumables | Planning |
| | Users can schedule Kills (end purges) or disable kills | Planning |
| | Users can define generic events and what script will actually be added to the master script (if needed) | Planning |
| | Mission plan generation will include a puck loading list | Planning |
| | User can associate external files with events (excel spreadsheet, documents, etc.) | Planning, Data Management |
| | Tide and phase information will be available | Planning, Data Management |
| | Application will list sample volumes with protocol run | Planning, Data Management |
| | User can add non-phase/protocol events (user defined) to the calendar anywhere | Data Management |
| | User can view images associated with phases | Data Management |
| | User can browse the .GAL file along with image and filter paper information | Data Management |
| | User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density | Data Management |
| | User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery | Data Management |
| | When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown | Data Management |
| | Application should allow for details of flushes to be seen/accounted for | Data Management |
| | The application should archive (and make available) the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts | Data Management |
| | Users should be able to download instrument logs and images and the GUI will parse out the following events:
* Track deployments of contextual sensors (sub-deployments of ESP)
* Collection of contextual sensor data (with capability to view/work with data) 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time | Data Management, State Visualization |
| | Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power | State Visualization |
| | Users can visualize the current state of the instrument | State Visualization |
| | Users can scroll back in time and visualize instrument state at the various points in time | State Visualization |

h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Glossary]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
# [01/11/2012 *GUI Update and Planning Meeting|2011_01_12]
{panel}
{column}
{section}
]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris S., Jim, Kevin, Brent, Doug, Wayne, Scott
Absent:&nbsp;&nbsp; Addie (maternity)


h3.


h3. Machine Builds

* &nbsp;

h3. MFB

* &nbsp;

h3. Software

* &nbsp;

h3. DWSM


h6. +Sphere+
\\

h6. +Elevator+

* &nbsp;

*{+}DWSM{+}*
* &nbsp;

h3.


h3. Other Items:

* &nbsp;]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Bill, Elif, Chris P, Julie, Jim, Roman

h3. &nbsp;Items:

&nbsp;1.&nbsp; JdF
* Ball had to be reopened to switch a communications pin.&nbsp; Will use this time to reload some testing pucks.&nbsp; Will not change PCR reagents.&nbsp; Will re-seal later today.&nbsp;
* Doug planning on test tank Weds.

2.&nbsp; Drifter
* Julie working on MFB 1.&nbsp; Her assays have been qualified on another MFB, so currently concentrating on being able to filter 2L, and what this does to the SPE efficiency, etc.&nbsp; Should be getting Hawaii water end of this week.&nbsp; Will test with that and higher-pressure pressure pots.&nbsp;

3.&nbsp; Roman concentrating on array needs.&nbsp; Will work with Julie and Chris P. for arrays for Hawaii and SC Wharf, respectively.&nbsp;
* ESP-Bruce recovered and will be shipped back to MBARI July 11.&nbsp;&nbsp;
* TTLab will start to get reorganized.&nbsp; Helpful in build of Betty and re-build of NEO.
* Chris P., will be needing help with the NEO conversion and will rely on Roman and Bill for the script re-do's she can't get to.

4.&nbsp; Elif has rec'd the SYBR assays, and will load on MFB 5 Friday or Monday with Preston help.&nbsp; She's trying to get assays ready for potentially a M0 deployemnt in Fall, although this has not been confirmed.

5.&nbsp; Bill testing MFB recovery of DNA with Qiagen wash buffer.&nbsp; Also has got MFB4 assembled from parts of others;&nbsp; still needs calibrating, both plumbing and heater module.\\]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Chris P, Chris S., Elif, Roman, Bill U.

h4. Items:

# Cold testing for WHOI deployment.
## Elif has compared old wash buffer with 'modified' wash (50% wash, 50% buffer E) (at 2 degrees, viscosity of wash \~10, modified wash \~3)
### blocking effciency on blank filter is similar
### signal with biomaterial similar (BAC arrays)
### moving to test HAB culture; if no difference, then moving to run HAB culture in cold.
### ESP-Bruce going into cold on Thursday.
# Array printing
## Roman planning a massive, 1-week printing run in early Feb.&nbsp; Will try and knock out all WHOI arrays.

3.  Discussion about using an unbuilt MFB for G3 development.&nbsp; Each missing some parts.&nbsp; Must talk to Chris P before building to know what needs to be done.]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit+\] &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# &nbsp;[Jan 4]
# &nbsp;
\\]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments]]></property>
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<property name="body"><![CDATA[h3. Machine Builds

* G


h3. MFB


h3.

* &nbsp;

h3. Drifter

* Gements.

h3. Software

* &nbsp;Bitive.

h3. Deep ESP


h6. +Sphere+

* Pas

h6. +Elevator+

* el bldg D.

*{+}DWSM{+}*
* Sw
** ed.

h3. GUI

* &nbsp;Br.

h3. Deployment Issues

* &nbsp;AprK (with new lo]]></property>
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<property name="body"><![CDATA[Present:

h3. &nbsp;Items
\\

1. &nbsp; ]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# CVS client
# gcc
# yacc

h3. Steps to build and run

# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:
{code}
cvs checkout ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.
{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This will populate the patch directory with the ruby source files without overwriting the patches.
# Now change directoies back to ../ruby-1.6.8 and run configure.
{code}
./configure
{code}
# Now run make.
{code}
make
{code}
# If all goes well, ruby will have built and you can install by running this as 'root'.
{code}
make install
{code}
# After that, ruby should be ready to go and if you type
{code}
ruby --version
{code}
You should see something like:
{code}
ruby 1.6.8-mbari7/0x4770 (2009-1-19) [i686-linux]
{code}
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites
# CVS client
# gcc
# yacc

h3. Steps to build and run
# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:{code}
cvs checkout ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This will populate the patch directory with the ruby source files without overwriting the patches.
# Now run configure.{code}
./configure
{code}
# Now run make.{code}
make
{code}
# If all goes well, ruby will have built and you can install by running this as 'root'.{code}
make install
{code}
# After that, ruby should be ready to go and if you type{code}
ruby --version
{code}
You should see something like:{code}
ruby 1.6.8-mbari7/0x4770 (2009-1-19) [i686-linux]
{code}
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]
# [Apr 12] \-\- Roman at WHOI, Chris P Europe
# Apr 19
# [Apr 26]
# [May 10]
# [May 17]
# May 24 \-\- Roman at WHOI, Chris S at WHOI, Chris P out
# [Jun 14] \-\- This has link to lysate dilution page
# [Jun 21]]]></property>
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<property name="body"><![CDATA[{gliffy:name=table|space=ESPAPP|page=12Mar2009|pageid=9372226|align=left|size=L}
Present:&nbsp; Jim, Brent, Doug, Wayne, Cheri, Chris S., Scott, Kevin
Absent:&nbsp; Gene, Addie (maternity)

h3. Machine Builds

* &nbsp;Gordon and Betty.&nbsp; Cheri predicts 3 weeks to finish if hands don't give her too many problems
** Maxon stopped making old motors, and these new ones (with mylar cable) produce much less torque.&nbsp; Maybe windings are for higher voltage.&nbsp; Cheri will test.&nbsp; We currently have 1 old motor and 3 new ones.
** We ordered 2 more harmonic drives.&nbsp; Moe has GG's lower hand and it will need to be changed out.

h3.


h3.


h3. MFB


h3.

* 3 MFB's have been shipped to McLane for build.
* Spoke with LLNL yesterday.&nbsp; John promised 2 modules by March 20 (2009).&nbsp; Then 4 by end of April, then 4 remaining 'after' that.&nbsp; New modules have different firmware (v 4.04 vs 4.03), so we'll have to get our two switched eventually.&nbsp; New firmware expands the data buffer and has better error handling.

h3. Drifter

* Gene out today.&nbsp; Wayne will start communications testing next week.&nbsp; Not using TCP, so this might be a problem.&nbsp; Will go with freewave modems (not iridium) and GPS for the drifter deployments.

h3. Software

* &nbsp;Bruce has been running the new software off the network for several weeks with no problems.&nbsp; Monday Brent will burn this software into Bruce's flash, and we'll start exercising it as a local machine.
* Much discussion about Bufflehead being full and Chris P losing data.&nbsp; We need a science data-manager (John Ryan?).&nbsp; Currently need to delete old stuff.
* Today, Brent will backup and delete stuff older than 1 year.
* Jim will go to IS to see if we can get more space on the ESPshare, although cost may be prohibitive.

h3. Deep ESP


h6. +Sphere+

* Paul Coenen continues with wiring.
* Vicor mounting brackets are finished.&nbsp; Assembly continues

h6. +Elevator+

* elevator is back from LA, but there may be some distortion.&nbsp; Doug going out for a look this PM.
* We can finish elevator construction with Mike Conway and Paul Coenen.
* Scott will move foam and other crated sphere half out of parking lot and into bldg D.

*{+}DWSM{+}*
* Switch boards are finished and we'll give to Wayne after this meeting so he can test his dPress code.&nbsp; Then we can put bags in oil.
* High pressure pump.&nbsp; Still waiting for return from Emeryville.&nbsp; 4500psi will get us to 3000m.&nbsp; We have a fall-back site if we need to go to only 1800m.
** During the 'repair', some parts were re-machined, thus we hope that fixed things.&nbsp; We will tighten bolts on current pump we have hoping that will stop back-flow above 2000psi.
** If nothing works, our options are to go to shallower sites where not as much pressure is needed.

h3. GUI

* &nbsp;Brian has begun work on image analysis software.&nbsp; Working with Nilo.
* Rich coming back to project to work on parsing data files.

h3. Deployment Issues

* &nbsp;April 1-28 surface deployment using BRUCE.&nbsp; Roman will get divers and is leading this Zephyr deployment.
* April 7, 14, May 1 \-\- Deep ESP tests using MACK (with new low-temp syringe plungers).
* May 12-June 11 surface deployment using MOE w/PCR (if ready).

h4.


h4. Crews

Zephyr surface:&nbsp; Chris S, Roman, Nilo, Cheri

June 5-9 Flyer:&nbsp; Chris S. Jim, Doug, Scott, Brent, Gene, Chris P., Roman, Julie, (Vrijenhoek), summer student

August 15-27 Flyer:&nbsp; Chris S., Doug, Scott, Brent, Chris P.
\\

h3. Other Items:

* &nbsp;Van is level and external power connections finished.&nbsp; Still must be wired internally.
* Chris S and Julie at CMORE in Hawaii next week; gone March 15-19.
* Jim will be gone at ASTID reviews March 30-April 3.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Doug, Wayne, Cheri, Chris S., Scott, Kevin
Absent:&nbsp; Gene, Addie (maternity)

h3. Machine Builds

* &nbsp;Gordon and Betty.&nbsp; Cheri predicts 3 weeks to finish if hands don't give her too many problems
** Maxon stopped making old motors, and these new ones (with mylar cable) produce much less torque.&nbsp; Maybe windings are for higher voltage.&nbsp; Cheri will test.&nbsp; We currently have 1 old motor and 3 new ones.
** We ordered 2 more harmonic drives.&nbsp; Moe has GG's lower hand and it will need to be changed out.

h3.


h3.


h3. MFB


h3.

* 3 MFB's have been shipped to McLane for build.
* Spoke with LLNL yesterday.&nbsp; John promised 2 modules by March 20 (2009).&nbsp; Then 4 by end of April, then 4 remaining 'after' that.&nbsp; New modules have different firmware (v 4.04 vs 4.03), so we'll have to get our two switched eventually.&nbsp; New firmware expands the data buffer and has better error handling.

h3. Drifter

* Gene out today.&nbsp; Wayne will start communications testing next week.&nbsp; Not using TCP, so this might be a problem.&nbsp; Will go with freewave modems (not iridium) and GPS for the drifter deployments.

h3. Software

* &nbsp;Bruce has been running the new software off the network for several weeks with no problems.&nbsp; Monday Brent will burn this software into Bruce's flash, and we'll start exercising it as a local machine.
* Much discussion about Bufflehead being full and Chris P losing data.&nbsp; We need a science data-manager (John Ryan?).&nbsp; Currently need to delete old stuff.
* Today, Brent will backup and delete stuff older than 1 year.
* Jim will go to IS to see if we can get more space on the ESPshare, although cost may be prohibitive.

h3. Deep ESP


h6. +Sphere+

* Paul Coenen continues with wiring.
* Vicor mounting brackets are finished.&nbsp; Assembly continues

h6. +Elevator+

* elevator is back from LA, but there may be some distortion.&nbsp; Doug going out for a look this PM.
* We can finish elevator construction with Mike Conway and Paul Coenen.
* Scott will move foam and other crated sphere half out of parking lot and into bldg D.

*{+}DWSM{+}*
* Switch boards are finished and we'll give to Wayne after this meeting so he can test his dPress code.&nbsp; Then we can put bags in oil.
* High pressure pump.&nbsp; Still waiting for return from Emeryville.&nbsp; 4500psi will get us to 3000m.&nbsp; We have a fall-back site if we need to go to only 1800m.
** During the 'repair', some parts were re-machined, thus we hope that fixed things.&nbsp; We will tighten bolts on current pump we have hoping that will stop back-flow above 2000psi.
** If nothing works, our options are to go to shallower sites where not as much pressure is needed.

h3. GUI

* &nbsp;Brian has begun work on image analysis software.&nbsp; Working with Nilo.
* Rich coming back to project to work on parsing data files.

h3. Deployment Issues

* &nbsp;April 1-28 surface deployment using BRUCE.&nbsp; Roman will get divers and is leading this Zephyr deployment.
* April 7, 14, May 1 \-\- Deep ESP tests using MACK (with new low-temp syringe plungers).
* May 12-June 11 surface deployment using MOE w/PCR (if ready).

h4.


h4. Crews

Zephyr surface:&nbsp; Chris S, Roman, Nilo, Cheri

June 5-9 Flyer:&nbsp; Chris S. Jim, Doug, Scott, Brent, Gene, Chris P., Roman, Julie, (Vrijenhoek), summer student

August 15-27 Flyer:&nbsp; Chris S., Doug, Scott, Brent, Chris P.
\\

h3. Other Items:

* &nbsp;Van is level and external power connections finished.&nbsp; Still must be wired internally.
* Chris S and Julie at CMORE in Hawaii next week; gone March 15-19.
* Jim will be gone at ASTID reviews March 30-April 3.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Doug, Wayne, Cheri, Chris S., Scott, Kevin
Absent:&nbsp; Gene, Addie (maternity)

h3. Machine Builds

* &nbsp;Gordon and Betty.&nbsp; Cheri predicts 3 weeks to finish if hands don't give her too many problems
** Maxon stopped making old motors, and these new ones (with mylar cable) produce much less torque.&nbsp; Maybe windings are for higher voltage.&nbsp; Cheri will test.&nbsp; We currently have 1 old motor and 3 new ones.
** We ordered 2 more harmonic drives.&nbsp; Moe has GG's lower hand and it will need to be changed out.

h3.


h3.


h3. MFB


h3.

* 3 MFB's have been shipped to McLane for build.
* Spoke with LLNL yesterday.&nbsp; John promised 2 modules by March 20 (2009).&nbsp; Then 4 by end of April, then 4 remaining 'after' that.&nbsp; New modules have different firmware (v 4.04 vs 4.03), so we'll have to get our two switched eventually.&nbsp; New firmware expands the data buffer and has better error handling.

h3. Drifter

* Gene out today.&nbsp; Wayne will start communications testing next week.&nbsp; Not using TCP, so this might be a problem.&nbsp; Will go with freewave modems (not iridium) and GPS for the drifter deployments.

h3. Software

* &nbsp;Bruce has been running the new software off the network for several weeks with no problems.&nbsp; Monday Brent will burn this software into Bruce's flash, and we'll start exercising it as a local machine.
* Much discussion about Bufflehead being full and Chris P losing data.&nbsp; We need a science data-manager (John Ryan?).&nbsp; Currently need to delete old stuff.
* Today, Brent will backup and delete stuff older than 1 year.
* Jim will go to IS to see if we can get more space on the ESPshare, although cost may be prohibitive.

h3. Deep ESP


h6. +Sphere+

* Paul Coenen continues with wiring.
* Vicor mounting brackets are finished.&nbsp; Assembly continues

h6. +Elevator+

* elevator is back from LA, but there may be some distortion.&nbsp; Doug going out for a look this PM.
* We can finish elevator construction with Mike Conway and Paul Coenen.
* Scott will move foam and other crated sphere half out of parking lot and into bldg D.

*{+}DWSM{+}*
* Switch boards are finished and we'll give to Wayne after this meeting so he can test his dPress code.&nbsp; Then we can put bags in oil.
* High pressure pump.&nbsp; Still waiting for return from Emeryville.&nbsp; 4500psi will get us to 3000m.&nbsp; We have a fall-back site if we need to go to only 1800m.
** During the 'repair', some parts were re-machined, thus we hope that fixed things.&nbsp; We will tighten bolts on current pump we have hoping that will stop back-flow above 2000psi.
** If nothing works, our options are to go to shallower sites where not as much pressure is needed.

h3. GUI

* &nbsp;Brian has begun work on image analysis software.&nbsp; Working with Nilo.
* Rich coming back to project to work on parsing data files.

h3. Deployment Issues

* &nbsp;April 1-28 surface deployment using BRUCE.&nbsp; Roman will get divers and is leading this Zephyr deployment.
* April 7, 14, May 1 \-\- Deep ESP tests using MACK (with new low-temp syringe plungers).
* May 12-June 11 surface deployment using MOE w/PCR (if ready).

h4. {gliffy:name=table\|space=ESPAPP\|page=12Mar2009\|pageid=9372226\|align=left\|size=L}


h4. Crews

Zephyr surface:&nbsp; Chris S, Roman, Nilo, Cheri

June 5-9 Flyer:&nbsp; Chris S. Jim, Doug, Scott, Brent, Gene, Chris P., Roman, Julie, (Vrijenhoek), summer student

August 15-27 Flyer:&nbsp; Chris S., Doug, Scott, Brent, Chris P.
\\

h3. Other Items:

* &nbsp;Van is level and external power connections finished.&nbsp; Still must be wired internally.
* Chris S and Julie at CMORE in Hawaii next week; gone March 15-19.
* Jim will be gone at ASTID reviews March 30-April 3.]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
\\
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage taken by Rob Vincent:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]

Map of locations:&nbsp; [http://maps.google.com/maps/ms?ie=UTF&msa=0&msid=213220825771739778963.0004a40bdd601babc291d]

May 23.&nbsp; Attempted recovery of ESP.&nbsp; Message from Roman:

{color:#996600}&nbsp;&nbsp;&nbsp; We went out to the site where espbruce was moored and attempted to find it.&nbsp; The weather was very poor and water was very turbid.&nbsp; Using the ships depth finder we found a promising target.&nbsp; In difficult conditions the divers performed a search but espbruce was not found.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; We recovered the mooring.&nbsp; It looks like the cable was pulled straight out of the cone.&nbsp; The top mast is bent but I cannot say if this was caused by a rough landing on the beach or boat impact.&nbsp; There are no dents or gouges on the mooring.&nbsp; The radio box is dry and antenna looks ok.{color}
{color:#996600}&nbsp;&nbsp;&nbsp; Thursday the RV Gulf Challenger may be able to survey the area with a side scanning sonar.&nbsp; This will be a much better way to search for espbruce.&nbsp;{color}

Message from Roman May 26:

{color:#996600}&nbsp;&nbsp;&nbsp; ESPbruce was located at&nbsp; 43° 02.0740 N&nbsp;&nbsp; 70° 36.8447 W at ~ 10m depth.&nbsp; This position is about 19 yards from the waypoint.&nbsp; So looks like it wasn't dragged and has maintained seal integrity.&nbsp; We will attempt to recover it this weekend if we can get the RV Tioga.&nbsp; If not will recover with the RV Connecticut on june 7th weather permitting.{color}
&nbsp;

Dates for a recovery kept moving as weather and scheduling problems arose.&nbsp; Finally, Roman reported on June 15:
{quote}
{quote}
{color:#996600} ESPbruce was recovered today with no visible external damage. The EM cable strain relief is still on the cable.&nbsp; The recovery operation used two ships the RV Gulf Challenger and it's sister the RV Tioga.&nbsp; The Challenger supported the the side scan survey and the Tioga supported the divers and lifting of the core package and its anchor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;The side scan sonar operator advised me at the beginning of the day that he believed the esp package would be found on the bottom.&nbsp; He based this opinion on the data secured by his colleague almost two weeks ago.&nbsp; From his read of that run, he believed that the instrument was 15m off the bottom at that time.&nbsp; Depth at this site is 49m.&nbsp; He felt that the instrument was slowly sinking and that by today it was surly be on the sea floor.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Todays side scan survey took approximately 90 minutes.&nbsp; They had acquired a strong signature on the core and calculated that it was at a depth of 65 feet (~20m). The package&nbsp; was still located within 10m of the original deployment site.&nbsp; They dropped a marker line with a float as close to the calculated position as possible.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;At this point divers equipped with twin 80 cu ft Nitrox cylinders and electric scooters dived on the marker.&nbsp; They had 70 minutes of search time.&nbsp; After 42 minutes an orange sausage float attached to a spectra lift line appeared.&nbsp; Then 10 minutes later a second lift bag attached to the EM cable appeared.&nbsp; The divers surfaced after a total bottom time of 62 minutes.&nbsp; Eight minutes to spare.&nbsp; We recovered the divers.&nbsp; They reported that the depth of top of the can was at 26 feet (~8m) right where it was supposed to be.{color}
{color:#996600}&nbsp;&nbsp; &nbsp;Recovery went smoothly using a single winch equipped with a capstan attachment.&nbsp; By alternately shifting the load from drum (used to lift anchor) and capstan (used to lift instrument we recovered the package and the anchor safely.{color}
{quote}
\\
\\  {color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford.
\\]]></property>
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<property name="body"><![CDATA[There is excellent, inverse correlation between T and NO3 in Mont Bay as Ken J and Luke C have shown.&nbsp; This probably is most robust in the spring....]]></property>
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<property name="body"><![CDATA[h3. Items:

1.&nbsp; Event Detection Discussion* Issues with event-detection on surface moorings are very complicated due to types of fluid-flow near the surface
* Much discussion on whether nitrate would be a better trigger for upwelling than temperature.&nbsp; Chris P. was asked if she can provide old ISUS and array data to see correlations.&nbsp; Yes she can.
* We will develop this for a surface deployment; logic will be on the ESP but thresholds will be adjustable from shore.
* We could also run this in 'test' mode, where it notifies shore that it should do something, and waits for instructions from humans.
* ACTION:&nbsp; We'll see how the data look to gain confidence we can get it to fire at the correct time.&nbsp;

2.&nbsp; D-ESP* D-ESP is now opened, unhooked from MARS simulator, and in the van.
* Need to know what housing we will deploy with the mass spec.&nbsp; Does it need different mounting brackes, etc.&nbsp; Bill to look into by contacting Peter.
* ISUS-\- the two deep ISUS housing have arrived.&nbsp; Doug will high-pressure test them the first 2 weeks of Feb.&nbsp; We still need to get the high-pressure probes ordered (Jim will ping Luke)
* Bill looked into turbidity issues at the 'Ashes' vent site.&nbsp; Unlikely we will need a 'prefilter' on the wand, but there may be issues with wand length.&nbsp; Must get requirements asap for any necessary development.
* Calendar is attached to last week's Engineering mtg notes.
&nbsp;3.&nbsp; Drifter comms* Brent has looked into Iridium phones and believes a solution exists to use these on Drifter (and an other mooring that needs to go Iridium).&nbsp; We are moving forward on getting a loaner phone here to test before purchase.
4.&nbsp; Spyglass* Although details are murky, Chris Melancon may have opportunity for contract work if anyone is interested.&nbsp; This would consist of being a tech-support 'lifeline' for newly sold ESP units.&nbsp; Please talk to Jim if you have any interest in this.
5.&nbsp; WHOI* WHOI phone conference tomorrow at 11 to discuss EOM mooring design.&nbsp; We will have a preliminary mtg today at 2 to discuss the issues before tomorrow's phone call.
* &nbsp;When we ship our mooring to WHOI, we will be using old DSP&L (orange) battery boxes (with alkalines), not the new tubes we are developing.\\]]></property>
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<property name="body"><![CDATA[h2. Items:
\\

&nbsp;1.&nbsp; MARS testing end date.&nbsp; Will unhook next Tuesday.&nbsp; We have not been able to make MARS gag again.&nbsp; Craig Dawe would like us to go completely to 375V, so we can go back on the same port.&nbsp; We may retain 48V so we can talk to it, should the 375V go down.\\

2.&nbsp; About 1.5 weeks left to perform MARS clean-up.\\

3.&nbsp; Shop has lost a person, and water jet is down, thus very busy.&nbsp; New CNC arriving in Feb.\\

4.&nbsp; Reagents to be checked at Spyglass.&nbsp; The 0.1um filtered stuff has never been produced by them; we will probably send someone to oversee production.\\

5.&nbsp; Much discussion about JdF calendar.&nbsp; To be attached. ]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] \- first discussion of adaptive sampling strategies
# Mar 3 - CMORE Hawaii
# [Mar 10] \-\- wand schematic
# [Mar 17]
# [Mar 24]
# Mar 31 - team deploying MOE at M0; Brent at WHOI
# [Apr 7]
# [Apr 14]
# [Apr 21]\--wand schematic reminder...
# [Apr 28]\--D-ESP 2-Year Birthday Celebration\!\!&nbsp; (Poster is [here|^ESP Birthday Poster(smaller).pdf])
# May 5 \-\- Visit to ASU
# [May 12]
# [May 19]
# [May 26]
# [Jun 2]
# Jun 9
# Jun 16
# [Jun 23]]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Bill, Elif, Chris P., Roman, Doug, Nilo, Chris S., Scott, Jim

h2. Items


h4. Jdf

* Instrument is ready to go.&nbsp; Wed will load water to do post-transport QC.
* Packing logistics:
** gas bottles are aboard
** ESP-Betty will be loaded on ship in plexibox
** Bill working on MSDS's for silicone oils, battery oil, batteries, He, and N2
** Truck arrives Wed at 9am for loading.&nbsp; Will be met in Newport by Chris P. on Friday morning.&nbsp; Bill/Scott/Doug arrive in Newport late Sunday night.
* Mission Plan
** The starting plan is [HERE|^JdF_TimeLine_06_27_11.pdf|Mission Plan] and Ruby code is HERE.&nbsp; Weather and any number of unforseen events may cause on-the-fly changing.&nbsp; Good Luck\!\!]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Bill, Elif, Chris P., Roman, Doug, Nilo, Chris S., Scott, Jim

h2. Items


h4. Jdf

* Instrument is ready to go.&nbsp; Wed will load water to do post-transport QC.
* Packing logistics:
** gas bottles are aboard
** ESP-Betty will be loaded on ship in plexibox
** Bill working on MSDS's for silicone oils, battery oil, batteries, He, and N2
** Truck arrives Wed at 9am for loading.&nbsp; Will be met in Newport by Chris P. on Friday morning.&nbsp; Bill/Scott/Doug arrive in Newport late Sunday night.
* Mission Plan
** The starting plan is [HERE|Mission plan|JdF_Timeline_06_27_11.pdf] and Ruby code is HERE.&nbsp; Weather and any number of unforseen events may cause on-the-fly changing.&nbsp; Good Luck\!\!]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Bill, Elif, Chris P., Roman, Doug, Nilo, Chris S., Scott, Jim

h2. Items


h4. Jdf

* Instrument is ready to go.&nbsp; Wed will load water to do post-transport QC.
* Packing logistics:
** gas bottles are aboard
** ESP-Betty will be loaded on ship in plexibox
** Bill working on MSDS's for silicone oils, battery oil, batteries, He, and N2
** Truck arrives Wed at 9am for loading.&nbsp; Will be met in Newport by Chris P. on Friday morning.&nbsp; Bill/Scott/Doug arrive in Newport late Sunday night.
* Mission Plan
** The starting plan is [HERE|https://oceana.mbari.org/confluence/users/insertlink-draft-attachmentstab.action?currentspace=ESPAPP&formname=createpageform&fieldname=content&draftType=page&spaceKey=ESPAPP&mode=attachments#|Mission plan] and Ruby code is HERE.&nbsp; Weather and any number of unforseen events may cause on-the-fly changing.&nbsp; Good Luck\!\!]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Bill, Elif, Chris P., Roman, Doug, Nilo, Chris S., Scott, Jim

h2. Items


h4. Jdf

* Instrument is ready to go.&nbsp; Wed will load water to do post-transport QC.
* Packing logistics:
** gas bottles are aboard
** ESP-Betty will be loaded on ship in plexibox
** Bill working on MSDS's for silicone oils, battery oil, batteries, He, and N2
** Truck arrives Wed at 9am for loading.&nbsp; Will be met in Newport by Chris P. on Friday morning.&nbsp; Bill/Scott/Doug arrive in Newport late Sunday night.
* Mission Plan
** The starting plan is [HERE|^JdF_TimeLine_06_27_11.pdf|Mission Plan] and Ruby script is [HERE|^JdF_mission.txt.pdf|Ruby script].&nbsp; Weather and any number of unforseen events may cause on-the-fly changing.&nbsp; Good Luck\!\!

h4. Proposal planning

* Will check with engineers regarding travel and capital purchase items next year

]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Bill, Elif, Chris P., Roman, Doug, Nilo, Chris S., Scott, Jim

h2. Items


h4. Jdf

* Instrument is ready to go.&nbsp; Wed will load water to do post-transport QC.
* Packing logistics:
** gas bottles are aboard
** ESP-Betty will be loaded on ship in plexibox
** Bill working on MSDS's for silicone oils, battery oil, batteries, He, and N2
** Truck arrives Wed at 9am for loading.&nbsp; Will be met in Newport by Chris P. on Friday morning.&nbsp; Bill/Scott/Doug arrive in Newport late Sunday night.
* Mission Plan
** The starting plan is [HERE|^JdF_TimeLine_06_27_11.pdf|Mission Plan] and Ruby code is [HERE|^JdF_mission.txt.pdf|Ruby script].&nbsp; Weather and any number of unforseen events may cause on-the-fly changing.&nbsp; Good Luck\!\!]]></property>
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<property name="body"><![CDATA[h1. All dates 2011
\\
# [Jan 6]]]></property>
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<property name="body"><![CDATA[h3. ESP GUI Demo and Question and Answer Session

The purpose of this meeting is to show the progress to date on the ESP Data Management/Planning GUI and to use this demonstration to foster information gathering that can be used to both direct development and answer development questions.

h5. Agenda

# Introduction/Recap
# Demonstrate GUI to date
## How to start it.  Click here: [http://predator.shore.mbari.org/esp_gui/launch.jnlp]
## Should work on Java 1.5+
## Right now you will need to be connected to MBARI intranet (that will change to local laptop installation)
## Upper left is list of instruments and their associated deployment.  Default start is to have all displayed.
### Display selection tree functionality
## Year selection drives the overview calendar displayed below.
## The overview calendar always shows all deployments
## Click on overview calendar to select month of interest.
### This drives main calendar.
 

h5. Questions:
# GUI:
## Default is to have no deployments displayed.  Is that OK, or should have they all show up to begin with?
## Should I show all deployments on the overview calendar?
## Should consumables be decreasing meters and turn red on low?
## How much detail (zoom) do you want to see?
## Where do you want to edit phases/deployment (table/popup/etc.)?
# Mission Scripts:
## What is 'startTube' and how is it determined?
## What are the 'rules' around script construction? 

h5. Data needed
# List of all possible consumable resources:
## Instruments:
### Darlene
### GIGI
### NEO
## Lists of phases, protocols
### HAB
#### SH1
#### lyfil
#### SH2
#### WCR
### DA
#### DA1
#### Dalyfil
#### DA2
### BAC
#### SH1
#### lyfil
#### SH2
#### WCR
### invert
#### SH1
#### lyfil
#### SH2
#### WCR
### BACAR
#### WCR
### QC
#### WCR
## Details for phases:
### Max duration
## Details for protocols:
### Duration
### Delay to sample
## Consumable Types:
### Fix
### AgMeOH
### ab1
### ab2
### Lysis
### Dilutent
### Sig1
### Sig2
### Sig3
### Con 1:5000
### Sub 1
### Sub 2
### Wash
### CSR Flush
### CSV Flush
### PSR Flush
### Kill
### Waste
### Power
## Bags/Containers/Storage:
### How big are the capacities for the above consumables?
## Protocol Makeup
### For each of the phase/protocol combination, what consumables to they use and how much (i.e. recipies)

h5. Requests
# Link the colors of the instruments to the deployments
# Have the deployments disappear on the overall calendar as well as the main calendar
# Clean up the view on the overview calendar so they don't look so busy (remove protocols and phases)
# Darlene is no longer with us, just GG (or GiGi) and Neo.  But there should be three new instruments coming on line.
# In the details pane, there was a desire to put the sample volume right next to the protocol name.
# When you select a protocol line in the details pane, a tab should be available to show the contextual data (CTD, ISUS) for the time span of when the sample volume was drawn
# There was a desire to have the CTD data displayed like the tide data is displayed and some way to turn on/off view of it
# Look into the possibility of using jruby to generate the mission script so the generation could be done outside of the planning application and changed there instead of inside the planning app.
## As a side note, you need to know the start tube in order to generate the mission script and the start tube will not be known till after the instrument is loaded.  Question, can't we tell the user how to best load the instrument based on the deployment configuration?
# There was a bit of discussion on the consumables view and how to use it in the planning phase.  I think the following was the resulting desire:
## When creating a new plan (deployment), the consumables should simply show how much of each consumable is being predicted (ml, watts, waste generation)
## Then at some point, the instrument will be 'loaded' and the view should be changed/enable that shows the amount of consumables are available (maybe also show how much is predicted to be consumed).  A full load will show all progress bars as 100% (display will show appropriate units like ml or watts) and then the bars will decrease as the log file is read and the actual amounts consumed are known.
## There was also a desire to know how many of the different phases could be configured with the current state of the instrument.  This speaks to the 'interrupted deployment scenario' where the instrument would be recovered and could be reconfigured (but no consumables added).  For example, if the instrument was recovered and it was half way through its consumption, the user could ask the application how many of the different phases could be run.  This would entail changing the pucks around, but the consumables would be left alone.  There was some talk about that just simply constituting a new 'deployment' since a new mission script would be created anyway.
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]
# [Apr 12] \-\- Roman at WHOI, Chris P Europe
# Apr 19
# [Apr 26]
# [May 10]
# [May 17]
# May 24 \-\- Roman at WHOI, Chris S at WHOI, Chris P out
# [Jun 14] \-\- This has link to lysate dilution page
# [Jun 21]
# [Jun 28]]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Elif, Roman, Nilo, Chris S., Jim

{color:#ff0000}Roman on vacation Aug 1-14.{color}

{color:#ff0000}Chris S on vacation Jul 13-19.{color}


h2. Items


h4. ESP-Bruce at WHOI

* &nbsp;We will have Bruce K. remove temp-sensitive reagents and FedEx to us, and we will ship equipment back in Unrefrigerated van ($5800 vs $9200).&nbsp; Because of Keafer's schedule, ESP will not be shipped until July 25.&nbsp; Roman sending Hobo temp sensor to see what temp swings the van experiences.
* We need to spot-check the ESP temp calibrations upon return, just to be sure.

h4. Pucks

* &nbsp;We have had 1200 puck pieces in need of serial number etching.&nbsp; We've rec'd the first 400 back from the etcher.&nbsp; Nilo is inspecting and will ready the next 800, probably in batches of 400.
* We've also rec'd pucks owed us from McLane (already serialized).&nbsp; These need to be inspected and Roman planning on doing lysis test with them.

h4. CTD

* &nbsp; Newly rebuilt fluorometer seems to give same readings as an old working model.&nbsp; Roman/Nilo doing an 'at-sea' test right now--I'm watching them out the window.
* We need to know the range the fluorometer needs for the clean water at Station Aloha.&nbsp; It may need 100x sensitivity.&nbsp; So, order of events:
*# Confirm {color:#0000cc}{*}CTD-4894{*}{color} is working
*# Call Kilo Muana for their CTD sensitivity settings
*# Call/send to Seabird to make the change
* Once drifter cruise is over, we will need to lower the gain for 'normal' use again.&nbsp; Next use may be the CA current drift in the Fall, 2011.

h4. Drifter Cruise

* We have the Shana Rae lined up for at-sea test either week of Aug8 or Aug15.
* Next Tuesday (Jul 19) we will meet with Julie & Roman to start _intense_ logistical planning.
* Chris would like to meet with Julie later in week to discuss:
*** All data collected so far on MFB related to drifter preparations
*** Progress on ISME paper
* Roman has array printing for this deployment completely under control.

h4. Sybr HAB Assay development

* &nbsp;at 400nm, results on ABI looked good.&nbsp; MFB look similar to AOAb.&nbsp; Raised primer concentration and got much better signal on MFB.
* Elif rec'd many cultures of various pseud's and is making plasmids, as these cultures have become difficult to get.

Wharf]]></property>
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<property name="body"><![CDATA[h3. ESP GUI Demo and Question and Answer Session

The purpose of this meeting is to show the progress to date on the ESP Data Management/Planning GUI and to use this demonstration to foster information gathering that can be used to both direct development and answer development questions.

h5. Agenda

* Introduction/Recap
* Demonstrate GUI to date
** How to start it.  Click here: [http://predator.shore.mbari.org/esp_gui/launch.jnlp]
** Should work on Java 1.5+
** Right now you will need to be connected to MBARI intranet (that will change to local laptop installation)
** Upper left is list of instruments and their associated deployment.  Default start is to have all displayed.
*** Display selection tree functionality
** Year selection drives the year context calendar displayed below.

* Questions:
* GUI:
** Default is to have all deployments of all instruments displayed.  Is that OK, or should have all disabled and user starts selecting?
* Mission Scripts:
** What is 'startTube' and how is it determined?
** ]]></property>
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<property name="body"><![CDATA[h3. ESP GUI Demo and Question and Answer Session

The purpose of this meeting is to show the progress to date on the ESP Data Management/Planning GUI and to use this demonstration to foster information gathering that can be used to both direct development and answer development questions.

h5. Agenda

* Introduction/Recap
* Demonstrate GUI to date
** How to start it.  Click here: 

* Questions:
* Mission Scripts:
** What is 'startTube' and how is it determined?
** ]]></property>
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<property name="body"><![CDATA[h3. ESP GUI Demo and Question and Answer Session

The purpose of this meeting is to show the progress to date on the ESP Data Management/Planning GUI and to use this demonstration to foster information gathering that can be used to both direct development and answer development questions.

h5. Agenda

# Introduction/Recap
# Demonstrate GUI to date
## How to start it.  Click here: [http://predator.shore.mbari.org/esp_gui/launch.jnlp]
## Should work on Java 1.5+
## Right now you will need to be connected to MBARI intranet (that will change to local laptop installation)
## Upper left is list of instruments and their associated deployment.  Default start is to have all displayed.
### Display selection tree functionality
## Year selection drives the overview calendar displayed below.
## The overview calendar always shows all deployments
## Click on overview calendar to select month of interest.
### This drives main calendar.
 

h5. Questions:
# GUI:
## Default is to have no deployments displayed.  Is that OK, or should have they all show up to begin with?
## Should I show all deployments on the overview calendar?
## Should consumables be decreasing meters and turn red on low?
# Mission Scripts:
## What is 'startTube' and how is it determined?
## What are the 'rules' around script construction? 

h5. Data needed
# List of all possible consumable resources:
## Instruments:
### Darlene
### GIGI
### NEO
## Lists of phases, protocols
### HAB
#### SH1
#### lyfil
#### SH2
#### WCR
### DA
#### DA1
#### Dalyfil
#### DA2
### BAC
#### SH1
#### lyfil
#### SH2
#### WCR
### invert
#### SH1
#### lyfil
#### SH2
#### WCR
### BACAR
#### WCR
### QC
#### WCR
## Details for phases:
### Max duration
## Details for protocols:
### Duration
### Delay to sample
## Consumable Types:
### Fix
### AgMeOH
### ab1
### ab2
### Lysis
### Dilutent
### Sig1
### Sig2
### Sig3
### Con 1:5000
### Sub 1
### Sub 2
### Wash
### CSR Flush
### CSV Flush
### PSR Flush
### Kill
### Waste
### Power
## Bags/Containers/Storage:
### How big are the capacities for the above consumables?
## Protocol Makeup
### For each of the phase/protocol combination, what consumables to they use and how much (i.e. recipies)

h5. Requests
]]></property>
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<property name="body"><![CDATA[h3. ESP GUI Demo and Question and Answer Session

The purpose of this meeting is to show the progress to date on the ESP Data Management/Planning GUI and to use this demonstration to foster information gathering that can be used to both direct development and answer development questions.

h5. Agenda

# Introduction/Recap
# Demonstrate GUI to date
## How to start it.  Click here: [http://predator.shore.mbari.org/esp_gui/launch.jnlp]
## Should work on Java 1.5+
## Right now you will need to be connected to MBARI intranet (that will change to local laptop installation)
## Upper left is list of instruments and their associated deployment.  Default start is to have all displayed.
### Display selection tree functionality
## Year selection drives the overview calendar displayed below.
## The overview calendar always shows all deployments
## Click on overview calendar to select month of interest.
### This drives main calendar.
 

h5. Questions:
# GUI:
## Default is to have no deployments displayed.  Is that OK, or should have they all show up to begin with?
## Should I show all deployments on the overview calendar?
## Should consumables be decreasing meters and turn red on low?
## How much detail (zoom) do you want to see?
## Where do you want to edit phases/deployment (table/popup/etc.)?
# Mission Scripts:
## What is 'startTube' and how is it determined?
## What are the 'rules' around script construction? 

h5. Data needed
# List of all possible consumable resources:
## Instruments:
### Darlene
### GIGI
### NEO
## Lists of phases, protocols
### HAB
#### SH1
#### lyfil
#### SH2
#### WCR
### DA
#### DA1
#### Dalyfil
#### DA2
### BAC
#### SH1
#### lyfil
#### SH2
#### WCR
### invert
#### SH1
#### lyfil
#### SH2
#### WCR
### BACAR
#### WCR
### QC
#### WCR
## Details for phases:
### Max duration
## Details for protocols:
### Duration
### Delay to sample
## Consumable Types:
### Fix
### AgMeOH
### ab1
### ab2
### Lysis
### Dilutent
### Sig1
### Sig2
### Sig3
### Con 1:5000
### Sub 1
### Sub 2
### Wash
### CSR Flush
### CSV Flush
### PSR Flush
### Kill
### Waste
### Power
## Bags/Containers/Storage:
### How big are the capacities for the above consumables?
## Protocol Makeup
### For each of the phase/protocol combination, what consumables to they use and how much (i.e. recipies)

h5. Requests
]]></property>
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<property name="body"><![CDATA[h3. ESP GUI Demo and Question and Answer Session

The purpose of this meeting is to show the progress to date on the ESP Data Management/Planning GUI and to use this demonstration to foster information gathering that can be used to both direct development and answer development questions.

h5. Agenda

* Introduction/Recap
* Demonstrate GUI to date
** How to start it.  Click here: [http://predator.shore.mbari.org/esp_gui/launch.jnlp]
** Should work on Java 1.5+
** Right now you will need to be connected to MBARI intranet (that will change to local laptop installation)
** Upper left is list of instruments and their associated deployment.  Default start is to have all displayed.
*** Display selection tree functionality
** Year selection drives the overview calendar displayed below.
** The overview calendar always shows all deployments
** Click on overview calendar to select month of interest.
*** This drives main calendar.
** 

h5. Questions:
* GUI:
** Default is to have no deployments displayed.  Is that OK, or should have they all show up to begin with?
** Should I show all deployments on the overview calendar?
**  
* Mission Scripts:
** What is 'startTube' and how is it determined?
** 

h5. Data needed
* List of all possible consumable resources:
** Bags:
*** 
h5. Requests
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<property name="body"><![CDATA[h3. ESP GUI Demo and Question and Answer Session

The purpose of this meeting is to show the progress to date on the ESP Data Management/Planning GUI and to use this demonstration to foster information gathering that can be used to both direct development and answer development questions.

h5. Agenda

# Introduction/Recap
# Demonstrate GUI to date
## How to start it.  Click here: [http://predator.shore.mbari.org/esp_gui/launch.jnlp]
## Should work on Java 1.5+
## Right now you will need to be connected to MBARI intranet (that will change to local laptop installation)
## Upper left is list of instruments and their associated deployment.  Default start is to have all displayed.
### Display selection tree functionality
## Year selection drives the overview calendar displayed below.
## The overview calendar always shows all deployments
## Click on overview calendar to select month of interest.
### This drives main calendar.
 

h5. Questions:
# GUI:
## Default is to have no deployments displayed.  Is that OK, or should have they all show up to begin with?
## Should I show all deployments on the overview calendar?
## Should consumables be decreasing meters and turn red on low?
# Mission Scripts:
## What is 'startTube' and how is it determined?
## What are the 'rules' around script construction? 

h5. Data needed
# List of all possible consumable resources:
## Instruments:
### Darlene
### GIGI
### NEO
## Lists of phases, protocols
### HAB
#### SH1
#### lyfil
#### SH2

### DA
### BAC
### invert
### BACAR
### QC
## Details for phases:
### Max duration
## Details for protocols:
### Duration
### Delay to sample

## Bags:
### 

h5. Requests
]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris S., Jim, Brent, Doug, Wayne, Scott, Cheri
Absent:&nbsp;&nbsp; Addie (maternity)

h3. Machine Builds

* &nbsp;Feb 23 Cheri finishes core builds and calibrations
* New battery connectors for surface-can lids have been ordered.

h3. MFB

* &nbsp;Cheri will ship 3 MFB kits to McLane tomorrow.&nbsp; Chris S. will cut PO to pay for assembly of 2 of them.&nbsp; Kits will not have instructions included.&nbsp; Tim can get copies of things when he's out next week for core assembly
* USCS people now finished with MFB01 and we can proceed with integration on MOE.&nbsp; Will do it the week of Feb 17; next week Scott will work on single connector, week after that Cheri can do mechanical merging.

h3. Software

* &nbsp;Ruby patch on all machines except MFB02, MFB03, Gordon, and Betty.
* Brent needs more cables:
** serial & debug cable (10-pin to DB9)
** PCR w/ level-shifter
** J-TAG cables
* Discussion about the need for more (newer?) laptops.&nbsp; Brent and Jim will talk to Todd.
* McLane needs one laptop that runs LINUS.&nbsp; (this typo purposely inserted to see who reads these notes).&nbsp; Again, will talk to Todd about getting a machine.
* Checksum difference--Wayne DID get correct bits eventually, so gave to DWSM and seems to be working.
* Wayne, Brent, Scott, Doug to meet at 10am tomorrow to discuss DWSM issues
* Wayne thinks 1 more day on dPress stuff and hardware and he'll be finished with DWSM hardware
* new Ethernet extenders shipped out today

h3. DWSM


h6. +Sphere+

* Sphere is approved to 4000m\!&nbsp; Hooray.
* MACK is designated core for Deep ESP tests.&nbsp; During June Flyer cruise, we will be using a new build (TBD).
* engineering will get&nbsp; MACK the week of Feb 23.
* Doug can fit any core into sphere, giving time to cold-test MACK
* Before that, GG will be cold tested in chamber to \-2C, then put syringes on Mack.\\

h6. +Elevator+

* &nbsp;CRP may be moving up their foam delivery date to mid-March due to some prior order cancellations
* It will need machining; still to determine who will do that
* Modem;&nbsp; we only have USBL transducers on the ships, but not lots of track record with this modem for both communications and release.&nbsp; Brent will talk to Dale Graves about this to help us decide what to go with.
* Although it's a back-burner issue, Doug will check with Flyer winch specs to see if it would be possible to use Spectra line to help place the D-ESP.

*{+}DWSM{+}*
* &nbsp;SeaConn will deliver elevator cable MARCH 13
* for wet-mate connector, we will use FOCE spare ODI connector--terminate exactly same way as on FOCE.
* Question as to whether the SIM-Can will go with us on the Northern Expedition.
* One pump on DWSM seems bad; Doug looking into getting replacement
* Brent will start working on DWSM control next week, after latest firmware on all dwarves.

h3. Other Items:

* &nbsp;light puck testing not yet finished
* Teflon retainers & O-rings--Chris S. hasn't done anything yet
* Need to re-machine puck top to accept new o-ring arrangement to hold against scintered frit.&nbsp; Doug to talk to Mark B/Mike Parker about this.
* Van.&nbsp; Will meet with Chris to discuss $$ for this.&nbsp; Needs to go down to 2 degrees C.]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# \[05Feb2009\]
# [12Feb2009]]]></property>
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</property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 -- no meeting; ASLO
# [05Feb2009]
# [12Feb2009]]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 -- no meeting; ASLO
# [05Feb2009[4Feb2009]] 
# [12Feb2009]]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 -- no meeting; ASLO
# [4Feb2009]]]></property>
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</property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] --First drifter attendance]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372224</id>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse the it to extract the its time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not wish to parse. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data{_}records.  Their formats conform to the following grammar:
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 #GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	#3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	#3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 #3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 #=tMAIN, =hcore, =ECan

gui_data = <`>actor?string		#see notes below
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	#switched to thread_name

`\Sam is cool			 	#There is an actor called 'S', so it must be escaped

`\Saturday symphony \

on the law \

in the park.				#multiline text
\\

*Tracking Log Time:*

\_timestamps:_Set the current log time.

If the timezone is specified, system is operating in real-time.

Real log time is Epoch seconds from Midnight 1/1/70 GMT.

If the timezone is omitted, system is operating in simulated time

Simulated log time is simply (simulated) seconds from simulation start.

\_time_increments:_Increment the current real or simulated log time.

_time_marks:_ Indicate the Real-time at which the entry was generated.

The timezone is always specified.

Does not alter the current log time.

Will only be generated if system is operating in simulated time mode.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\ \\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""
\\ \\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; end&nbsp; #case


end&nbsp; #loop]]></property>
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<id name="id">8945705</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse the it to extract the its time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not wish to parse. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data{_}records.  Their formats conform to the following grammar:\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 #GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>\\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	#3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	#3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 #3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 #=tMAIN, =hcore, =ECan

gui_data = <`>actor?string		#see notes below\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	#switched to thread_name

`\Sam is cool			 	#There is an actor called 'S', so it must be escaped

`\Saturday symphony \

on the law \

in the park.				#multiline text\\

*Tracking Log Time:*

\_timestamps:_Set the current log time.

If the timezone is specified, system is operating in real-time.

Real log time is Epoch seconds from Midnight 1/1/70 GMT.

If the timezone is omitted, system is operating in simulated time

Simulated log time is simply (simulated) seconds from simulation start.

\_time_increments:_Increment the current real or simulated log time.

_time_marks:_ Indicate the Real-time at which the entry was generated.

The timezone is always specified.

Does not alter the current log time.

Will only be generated if system is operating in simulated time mode.

Each log entry has a "context" that consists of its log time and the actor that wrote it.\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""\\

*GetNextGuiDataText():*
\\ <!-- 		@page { size: 8.5in 11in; margin: 0.79in } 		P { margin-bottom: 0.08in } 	-->GetNextGuiDataText:

loop do


&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

logTime = epoch seconds specified

if (zone specified)

timeZone=zone from timestamp

continue;

when time_increment:

logTime \+= specified increment

continue;

when alias:

if (string present)

actors\[moniker\] = string

else

actors.delete moniker

continue;

when gui_data:

c = character following <`>

if (c == <"> )

actor = text between quotes

else if (c == <\>)

return next character to end of entry

else if moniker\[c\] exists

actor = moniker\[c\]

return  next character to end of entry

else

return c + next character to end of entry

end

end]]></property>
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<id name="id">8945703</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse the it to extract the its time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not wish to parse. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data{_}records.  Their formats conform to the following grammar:

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 #GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	#3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	#3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 #3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 #=tMAIN, =hcore, =ECan

gui_data = <`>actor?string		#see notes below

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	#switched to thread_name

`\Sam is cool			 	#There is an actor called 'S', so it must be escaped

`\Saturday symphony \

on the law \

in the park.				#multiline text

*Tracking Log Time:*

\_timestamps:_Set the current log time.

If the timezone is specified, system is operating in real-time.

Real log time is Epoch seconds from Midnight 1/1/70 GMT.

If the timezone is omitted, system is operating in simulated time

Simulated log time is simply (simulated) seconds from simulation start.

\_time_increments:_Increment the current real or simulated log time.

_time_marks:_ Indicate the Real-time at which the entry was generated.

The timezone is always specified.

Does not alter the current log time.

Will only be generated if system is operating in simulated time mode.

Each log entry has a "context" that consists of its log time and the actor that wrote it.

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

*GetNextGuiDataText():*
\\]]></property>
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<id name="id">8945701</id>
<property name="body"><![CDATA[<!-- 		@page { size: 8.5in 11in; margin: 0.79in } 		P { margin-bottom: 0.08in } 	-This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse the it to extract the its time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not wish to parse. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data{_}records.  Their formats conform to the following grammar:

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 #GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	#3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	#3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 #3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 #=tMAIN, =hcore, =ECan

gui_data = <`>actor?string		#see notes below

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	#switched to thread_name

`\Sam is cool			 	#There is an actor called 'S', so it must be escaped

`\Saturday symphony \

on the law \

in the park.				#multiline text



*Tracking Log Time:*

_timestamps:_Set the current log time.

If the timezone is specified, system is operating in real-time.

Real log time is Epoch seconds from Midnight 1/1/70 GMT.

If the timezone is omitted, system is operating in simulated time

Simulated log time is simply (simulated) seconds from simulation start.

_time_increments:_Increment the current real or simulated log time.



_time_marks:_ Indicate the Real-time at which the entry was generated.

The timezone is always specified.

Does not alter the current log time.

Will only be generated if system is operating in simulated time mode.

Each log entry has a "context" that consists of its log time and the actor that wrote it.

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""





*GetNextGuiDataText():*

loop {

&nbsp;&nbsp;&nbsp; case (next entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; end

}]]></property>
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<id name="id">17891598</id>
<property name="body"><![CDATA[# [4K Sphere]
# [Sable 5000 Iridium Beacon Manual|^Xeos_Sable_manual.pdf|manual]]]></property>
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</property>
</object>
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<id name="id">8945714</id>
<property name="body"><![CDATA[In order to read in data from the ESP, the GUI will use the ESP's log (*real.log*) file as the official 'interface' for data collection.  In order to facilitate this, this page documents what the entries in the log file should look like so that the ESP GUI will not have to make extensive and fragile rules to try and interpret the data.  The log entries should have the following format:

*\@EPOCH_SECONDS\@<*_Thread_*>DATAMGMT,*_EVENT-NAME_*,*_attribute=value,..._

Notes:
# Time is designated using epoch seconds (number of seconds that have elapsed since January 1, 1970) in _GMT_
# EVENT_NAME is one of the following:
## BEGIN_MISSON
## PHASE_START
## PHASE_END
## PROTOCOL_START
## PROTOCOL_END
## SAMPLE_START
## SAMPLE_END
## CAMERA_SNAP
## END_MISSION
# Attributes are key=value pairs and vary from event to event.  Attributes for the various events are:
## BEGIN_MISSON
### No attributes
### Example: {{\@1231372399\@<Main>DATAMGMT,BEGIN_MISSION}}
## PHASE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### Example: {{\@1231372399\@<Main>DATAMGMT,PHASE_START,phase_name=hab}}
## PHASE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS (this is the time that the phase started.  This is necessary due to the fact there are multiple threads the name & start date are the unique key.)
### Example: {{\@1231372399\@<Main>DATAMGMT,PHASE_END,phase_name=hab,phase_start=1231372399}}
## PROTOCOL_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECDONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### Example: {{\@1231372399\@<Main>DATAMGMT,PROTOCOL_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1}}
## PROTOCOL_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### Example: {{\@1231372399\@<Main>DATAMGMT,PROTOCOL_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399}}
## SAMPLE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### target_volume=ZZZZml
### Example: {{\@1231372399\@<Main>DATAMGMT,SAMPLE_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,target_volume=1000ml}}
## SAMPLE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### sample_volume=ZZZZml
### Example: {{\@1231372399\@<Main>DATAMGMT,SAMPLE_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,sample_volume=934.1ml}}
## CAMERA_SNAP
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### file_name=ZZZZZZZZZ.tif
### auto_exposure=AAAAAAAs
### Example: {{\@1231372399\@<Main>DATAMGMT,CAMERA_SNAP,phase_name=hab,phase_start=1231372399,file_name=bac08oct1716h450ml40s.tif,auto_exposure=123.4s}}
]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">8945712</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse the it to extract the its time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not wish to parse. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data{_}records.  Their formats conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 #GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	#3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	#3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 #3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 #=tMAIN, =hcore, =ECan

gui_data = <`>actor?string		#see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	#switched to thread_name

`\Sam is cool			 	#There is an actor called 'S', so it must be escaped

`\Saturday symphony \

on the law \

in the park.				#multiline text
\\
\\

*Tracking Log Time:*

\_timestamps:_Set the current log time.

If the timezone is specified, system is operating in real-time.

Real log time is Epoch seconds from Midnight 1/1/70 GMT.

If the timezone is omitted, system is operating in simulated time

Simulated log time is simply (simulated) seconds from simulation start.

\_time_increments:_Increment the current real or simulated log time.

_time_marks:_ Indicate the Real-time at which the entry was generated.

The timezone is always specified.

Does not alter the current log time.

Will only be generated if system is operating in simulated time mode.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""
\\
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse the it to extract the its time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not wish to parse. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data{_}records.  Their formats conform to the following grammar:
\\ \\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 #GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\ \\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	#3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	#3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 #3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 #=tMAIN, =hcore, =ECan

gui_data = <`>actor?string		#see notes below
\\ \\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\ \\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	#switched to thread_name

`\Sam is cool			 	#There is an actor called 'S', so it must be escaped

`\Saturday symphony \

on the law \

in the park.				#multiline text
\\ \\

*Tracking Log Time:*

\_timestamps:_Set the current log time.

If the timezone is specified, system is operating in real-time.

Real log time is Epoch seconds from Midnight 1/1/70 GMT.

If the timezone is omitted, system is operating in simulated time

Simulated log time is simply (simulated) seconds from simulation start.

\_time_increments:_Increment the current real or simulated log time.

_time_marks:_ Indicate the Real-time at which the entry was generated.

The timezone is always specified.

Does not alter the current log time.

Will only be generated if system is operating in simulated time mode.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""
\\
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">8945722</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse the it to extract the its time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records.  Their formats conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	&nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	#switched to thread_name

`\Sam is cool			 	#There is an actor called 'S', so it must be escaped

`\Saturday symphony \

on the law \

in the park.				#multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.If the timezone is specified, system is operating in real-time.

Real log time is Epoch seconds from Midnight 1/1/70 GMT.

If the timezone is omitted, system is operating in simulated time

Simulated log time is simply (simulated) seconds from simulation start.
\\

_time_increments_:&nbsp; Increment the current real or simulated log time.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.The timezone is always specified.

Does not alter the current log time.

Will only be generated if system is operating in simulated time mode.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""
\\
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<id name="id">8945720</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse the it to extract the its time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not wish to parse. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data{_}records.  Their formats conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 #GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	#3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	#3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 #3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 #=tMAIN, =hcore, =ECan

gui_data = <`>actor?string		#see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	#switched to thread_name

`\Sam is cool			 	#There is an actor called 'S', so it must be escaped

`\Saturday symphony \

on the law \

in the park.				#multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.If the timezone is specified, system is operating in real-time.

Real log time is Epoch seconds from Midnight 1/1/70 GMT.

If the timezone is omitted, system is operating in simulated time

Simulated log time is simply (simulated) seconds from simulation start.\\

_time_increments_:&nbsp; Increment the current real or simulated log time.\\

_time_marks:_ Indicate the Real-time at which the entry was generated.The timezone is always specified.

Does not alter the current log time.

Will only be generated if system is operating in simulated time mode.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\ \\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""
\\
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<id name="id">8945717</id>
<property name="body"><![CDATA[In order to read in data from the ESP, the GUI will use the ESP's log (*real.log*) file as the official 'interface' for data collection.  In order to facilitate this, this page documents what the entries in the log file should look like so that the ESP GUI will not have to make extensive and fragile rules to try and interpret the data.  The esp gui log data should have the following format in the context the [raw log file|ESPAPP:Parsing the Raw ESP Log File Format|Raw Log File Format]:


*@EPOCH_SECONDS@<*{_}Thread{_}*>DATAMGMT,*{_}EVENT-NAME{_}*,*{_}attribute=value,..._

Notes:
# Time is designated using epoch seconds (number of seconds that have elapsed since January 1, 1970) in _GMT_
# EVENT_NAME is one of the following:
## BEGIN_MISSON
## PHASE_START
## PHASE_END
## PROTOCOL_START
## PROTOCOL_END
## SAMPLE_START
## SAMPLE_END
## CAMERA_SNAP
## END_MISSION
# Attributes are key=value pairs and vary from event to event.  Attributes for the various events are:
## BEGIN_MISSON
### No attributes
### Example: {{@1231372399@<Main>DATAMGMT,BEGIN_MISSION}}
## PHASE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### Example: {{@1231372399@<Main>DATAMGMT,PHASE_START,phase_name=hab}}
## PHASE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS (this is the time that the phase started.  This is necessary due to the fact there are multiple threads the name & start date are the unique key.)
### Example: {{@1231372399@<Main>DATAMGMT,PHASE_END,phase_name=hab,phase_start=1231372399}}
## PROTOCOL_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECDONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### Example: {{@1231372399@<Main>DATAMGMT,PROTOCOL_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1}}
## PROTOCOL_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### Example: {{@1231372399@<Main>DATAMGMT,PROTOCOL_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399}}
## SAMPLE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### target_volume=ZZZZml
### Example: {{@1231372399@<Main>DATAMGMT,SAMPLE_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,target_volume=1000ml}}
## SAMPLE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### sample_volume=ZZZZml
### Example: {{@1231372399@<Main>DATAMGMT,SAMPLE_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,sample_volume=934.1ml}}
## CAMERA_SNAP
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### file_name=ZZZZZZZZZ.tif
### auto_exposure=AAAAAAAs
### Example: {{@1231372399@<Main>DATAMGMT,CAMERA_SNAP,phase_name=hab,phase_start=1231372399,file_name=bac08oct1716h450ml40s.tif,auto_exposure=123.4s}}]]></property>
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<id name="id">8945730</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse the it to extract the its time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records.  Their formats conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	&nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.If the timezone is specified, system is operating in real-time.

Real log time is Epoch seconds from Midnight 1/1/70 GMT.

If the timezone is omitted, system is operating in simulated time

Simulated log time is simply (simulated) seconds from simulation start.
\\ \\

_time_increments_:&nbsp; Increment the current real or simulated log time.
\\ \\

_time_marks:_ Indicate the Real-time at which the entry was generated.The timezone is always specified.

Does not alter the current log time.

Will only be generated if system is operating in simulated time mode.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""
\\
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse the it to extract the its time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records.  Their formats conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	&nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.If the timezone is specified, system is operating in real-time.

Real log time is Epoch seconds from Midnight 1/1/70 GMT.

If the timezone is omitted, system is operating in simulated time

Simulated log time is simply (simulated) seconds from simulation start.
\\

_time_increments_:&nbsp; Increment the current real or simulated log time.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.The timezone is always specified.

Does not alter the current log time.

Will only be generated if system is operating in simulated time mode.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""
\\
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<id name="id">8945728</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse the it to extract the its time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records.  Their formats conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	&nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.If the timezone is specified, system is operating in real-time.

Real log time is Epoch seconds from Midnight 1/1/70 GMT.

If the timezone is omitted, system is operating in simulated time

Simulated log time is simply (simulated) seconds from simulation start.
\\

_time_increments_:&nbsp; Increment the current real or simulated log time.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.The timezone is always specified.

Does not alter the current log time.

Will only be generated if system is operating in simulated time mode.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""
\\
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse the it to extract the its time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records.  Their formats conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	&nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the law \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.If the timezone is specified, system is operating in real-time.

Real log time is Epoch seconds from Midnight 1/1/70 GMT.

If the timezone is omitted, system is operating in simulated time

Simulated log time is simply (simulated) seconds from simulation start.
\\

_time_increments_:&nbsp; Increment the current real or simulated log time.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.The timezone is always specified.

Does not alter the current log time.

Will only be generated if system is operating in simulated time mode.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""
\\
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse the it to extract the its time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records.  Their formats conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	&nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor called 'S', so it must be escaped

`\Saturday symphony \

on the law \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.If the timezone is specified, system is operating in real-time.

Real log time is Epoch seconds from Midnight 1/1/70 GMT.

If the timezone is omitted, system is operating in simulated time

Simulated log time is simply (simulated) seconds from simulation start.
\\

_time_increments_:&nbsp; Increment the current real or simulated log time.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.The timezone is always specified.

Does not alter the current log time.

Will only be generated if system is operating in simulated time mode.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""
\\
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering member to try to determine what the GUI needs to do.  The following requirements were gathered as part of that process:

h3. Requirements
{section}
{column:width=60%}
||Number||Requirement||Associated View||
|1|User can define missions by specifying phases|Planning|
|2|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|Be able to add non-phase/protocol events (user defined) to the calendar anywhere|Operation|
|5|Be able to set mission start end times that are not associated with a phase/protocol|Planning|
|6|Be able to specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User shall be able to add comments to a phase that will be generated in the script|Planning|
|8|User shall be able to view images associated with phases|Operation|
|9|User shall be able to browse the .GAL file along with image and filter paper information|Operation|
|10|User should be able to browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Operation|
|11|User should be able to browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Operation|
|12|User should be able to associate external files with events (excel spreadsheet, documents, etc.)|Planning,Operation|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|Operation|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users should have a form to add/delete/edit protocol runs and phases|Planning|
|16|Users should have a form to add/delete/edit consumables|Planning|
|17|In application users should have sample volume listed with protocol run|Planning|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should somehow be shown|Operation|
|19|Tide and phase information should be available during planning|Planning,Operation|
|20|Application should allow for details of flushes to be seen/accounted for|Operation|
|21|Users should be able to schedule Kills (end purges) or disable kills|Planning|
|22|Users should be able to define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to visualize the current state of the instrument|Operation,State|
|24|Users should be able to scroll back in time and visualize instrument state at the various points in time|State|
{column}
{column:width=40%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
{panel}
{panel:title=Supporting Docs}
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering member to try to determine what the GUI needs to do.  The following requirements were gathered as part of that process:

h3. Requirements
{section}
{column:width=60%}
||Number||Requirement||Associated View||
|1|User can define missions by specifying phases|Planning|
|2|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|Be able to add non-phase/protocol events (user defined) to the calendar anywhere|Operation|
|5|Be able to set mission start end times that are not associated with a phase/protocol|Planning|
|6|Be able to specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User shall be able to add comments to a phase that will be generated in the script|Planning|
|8|User shall be able to view images associated with phases|Operation|
|9|User shall be able to browse the .GAL file along with image and filter paper information|Operation|
|10|User should be able to browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Operation|
|11|User should be able to browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Operation|
|12|User should be able to associate external files with events (excel spreadsheet, documents, etc.)|Planning,Operation|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|Operation|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users should have a form to add/delete/edit protocol runs and phases|Planning|
|16|Users should have a form to add/delete/edit consumables|Planning|
|17|In application users should have sample volume listed with protocol run|Planning|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should somehow be shown|Operation|
|19|Tide and phase information should be available during planning|Planning,Operation|
|20|Application should allow for details of flushes to be seen/accounted for|Operation|
|21|Users should be able to schedule Kills (end purges) or disable kills|Planning|
|22|Users should be able to define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to download instrument logs and images and the GUI will parse out the following events: * Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time
|Operation|
|24|Users should be able to visualize the current state of the instrument|Operation,State|
|25|Users should be able to scroll back in time and visualize instrument state at the various points in time|State|
{column}
{column:width=40%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
{panel}
{panel:title=Supporting Docs}
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[# [08Jan2009]]]></property>
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<property name="body"><![CDATA[Present:
Absent:&nbsp;&nbsp; Addie (maternity)

h3.


h3. Machine Builds

* &nbsp;

h3. MFB

* &nbsp;

h3. Software

* &nbsp;

h3. DWSM


h6. +Sphere+

* &nbsp;

h6. +Elevator+

* &nbsp;

*{+}DWSM{+}*

h3. GUI Development

* &nbsp;

h3. Other Items:

* &nbsp;]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris S., Jim, Kevin, Brent, Doug, Wayne, Scott
Absent:&nbsp;&nbsp; Addie (maternity), Cheri

h3.


h3. Machine Builds

* Weeks of Feb 8 and Feb 23 are on for the McLane core builds.&nbsp; Chris S. will confirm with Tim.

h3. MFB

* &nbsp;Cheri will be finished with core kitting by Friday.&nbsp; Then its on to MFB kitting.&nbsp; Goal is to send to McLane by Feb 8.&nbsp; McLane will do tubing cutting.&nbsp; We will update this schedule the 1st week of Feb.

h3. Software

* &nbsp;New Ruby patch (R7) has checked out on Moe.&nbsp; Next Thursday will install on Mack/Bruce/Neo.
* Brent's Ruby patches have been adopted by the gods of Ruby, the Japanese. (This is a big deal, that he should bring to his 2009 review\!)
* New puck handling code will be installed with the R7 patch.&nbsp; Now the hand will move a little closer to the pucks when positioned over the carousel to make sure the hand closes on the puck.
* Brent is modifying the log file formats so less CPU time is spent parsing the date /time stamps.&nbsp; He explains this [here|ESPAPP:Parsing the Raw ESP Log File Format].

h3. DWSM


h6. +Sphere+

* Doug has created PO for SWRI
* Will ask Cindy to organize trip to SWRI

h6. +Elevator+

* &nbsp;Mike P. still working on drawings, but unknown progress
* John Erickson still analyzing frame, but coming up with screwy numbers; model may be wrong.
* FOAM:&nbsp; Trellenberg being difficult and now saying delivery is March 30-April3.&nbsp; We have several workaround options:
** Mike Conway says they (DMO) have 12 ft^3 (or more) of 34lb foam we may be able to use
** This amount may only allow 4 batteries and maybe no CTD
** Could supplement with glass spheres, but there is a 6-8 wk lead and possible redesign of float housing to accommodate.
** DECISION:
*** Will use 'Mike" foam and supplement with FOCE foam or use some of Ken Smith's 40lb foam.
* Modem on elevator:&nbsp; nice to have so we can ping without having ROV to plug in.&nbsp; Deck boxes; who has them--we may need to purchase.

*{+}DWSM{+}*
* Have been running pumps and looks like we will be able to get 6000psi out of them.
* Intake exhaust is running--energy draw is within design limits
* CABLES--critical path issue.&nbsp; 8 week lead time from Seaconn;&nbsp; Scott trying to push them, especially on terminations, but they are rigid in time estimate.&nbsp; Unclear if the 8 weeks is with or without terminations.&nbsp; Will keep checking in with them.

h3. &nbsp;

GUI Development
* &nbsp;

h3. Other Items:

* &nbsp;For March and April sphere deployments, we will use MACK.&nbsp; In May will decide which core to mount with PCR.]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [21Jan2009]]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse the it to extract the its time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records.  Their formats conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	&nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.If the timezone is specified, system is operating in real-time.Real log time is Epoch seconds from Midnight 1/1/70 GMT.

If the timezone is omitted, system is operating in simulated time

Simulated log time is simply (simulated) seconds from simulation start.
\\

\\

_time_increments_:&nbsp; Increment the current real or simulated log time.
\\
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.The timezone is always specified.Does not alter the current log time.Will only be generated if system is operating in simulated time mode.\\

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""
\\
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse the it to extract the its time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records.  Their formats conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	&nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
\\

_time_increments_:&nbsp; Increment the current real or simulated log time.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.
* Will only be generated if system is operating in simulated time mode.\\

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""
\\
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering member to try to determine what the GUI needs to do.  The following requirements were gathered as part of that process:

h3. Requirements
{section}
{column:width=60%}
||Number||Requirement||Associated View||
|1|User can define missions by specifying phases|Planning|
|2|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|Be able to add non-phase/protocol events (user defined) to the calendar anywhere|Operation|
|5|Be able to set mission start end times that are not associated with a phase/protocol|Planning|
|6|Be able to specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User shall be able to add comments to a phase that will be generated in the script|Planning|
|8|User shall be able to view images associated with phases|Operation|
|9|User shall be able to browse the .GAL file along with image and filter paper information|Operation|
|10|User should be able to browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Operation|
|11|User should be able to browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Operation|
|12|User should be able to associate external files with events (excel spreadsheet, documents, etc.)|Planning,Operation|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|Operation|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users should have a form to add/delete/edit protocol runs and phases|Planning|
|16|Users should have a form to add/delete/edit consumables|Planning|
|17|In application users should have sample volume listed with protocol run|Planning|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should somehow be shown|Operation|
|19|Tide and phase information should be available during planning|Planning,Operation|
|20|Application should allow for details of flushes to be seen/accounted for|Operation|
|21|Users should be able to schedule Kills (end purges) or disable kills|Planning|
|22|Users should be able to define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to download instrument logs and images and the GUI will parse out the following events: 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time|Operation|
|24|Users should be able to visualize the current state of the instrument|Operation,State|
|25|Users should be able to scroll back in time and visualize instrument state at the various points in time|State|
{column}
{column:width=40%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
{panel}
{panel:title=Supporting Docs}
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering member to try to determine what the GUI needs to do.  The following requirements were gathered as part of that process:

h3. Requirements
{section}
{column:width=60%}
||Number||Requirement||Associated View||
|1|User can define missions by specifying phases|Planning|
|2|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|Be able to add non-phase/protocol events (user defined) to the calendar anywhere|Operation|
|5|Be able to set mission start end times that are not associated with a phase/protocol|Planning|
|6|Be able to specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User shall be able to add comments to a phase that will be generated in the script|Planning|
|8|User shall be able to view images associated with phases|Operation|
|9|User shall be able to browse the .GAL file along with image and filter paper information|Operation|
|10|User should be able to browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Operation|
|11|User should be able to browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Operation|
|12|User should be able to associate external files with events (excel spreadsheet, documents, etc.)|Planning,Operation|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|Operation|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users should have a form to add/delete/edit protocol runs and phases|Planning|
|16|Users should have a form to add/delete/edit consumables|Planning|
|17|In application users should have sample volume listed with protocol run|Planning|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should somehow be shown|Operation|
|19|Tide and phase information should be available during planning|Planning,Operation|
|20|Application should allow for details of flushes to be seen/accounted for|Operation|
|21|Users should be able to schedule Kills (end purges) or disable kills|Planning|
|22|Users should be able to define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to download instrument logs and images and the GUI will parse out the following events: 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time|Operation|
|24|Users should be able to visualize the current state of the instrument|Operation,State|
|25|Users should be able to scroll back in time and visualize instrument state at the various points in time|State|
{column}
{column:width=40%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting|2009_01_22]
{panel}
{panel:title=Supporting Docs}
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[This was a meeting that the GUI team held to get back on track for development for 2009.]]></property>
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<property name="body"><![CDATA[This was a meeting that the GUI team held to get back on track for development for 2009.
{section}
{column:width=60%}
{column}
{column:width=40%}
{panel}
{panel}
{column}
{section}]]></property>
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</property>
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<property name="body"><![CDATA[This was a meeting that the GUI team held to get back on track for development for 2009.
{section}
{column:width=60%}
{column}
{column:width=40%}
{panel:title=Attendees}
* Kevin Gomes
* Brian Schlining
* Rich Schramm
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h3. Minutes
This was a meeting that the GUI team held to get back on track for development for 2009.
{section}
{column:width=60%}
h5. Status update
GUI is being used for planning and some data processing.  The log file parsing is creating all kinds of issues with application deployment due to the Ruby requirements.  Brent is OK with changing to log file to allow us to rip out the Ruby stuff which should fix deployment issues.
h5. Log file processing
Brent was OK with us putting in log entries however we wanted.  He will be tagging all log entries with an epoch seconds offset from a base timestamp further up the log file.  That should work OK because we can put fully atomic log entries in our entries. Rich will work on the ruby code and Kevin will work on the GUI to consume those.  Not sure how we will implement, integrate and test the changes.  Kevin will talk to Brent.

h5. Image analysis
Brian will be working on the ESP stuff in March and he wanted to make sure that it is known that he may only get to a point where he understands the problem based on the days he was given.  He currently has software that will find spots and calculate intensity.  He can find and label spots with intensity.

The issue is taking the report from the filter paper print job and align the image with that map.  Once this is done, the rest should move forward, but this alignment, scaling, rotation is the key issue.  There are products out there that do this type of analysis, but they are commercial and proprietary.

The goal of this work will be to have an image in the GUI with the spot map overlayed and a key that has the various spots and their labels with their intensity.  This could then all be saved off to a text file for analysis/import.

h5. Action items
# Kevin to talk to Brent about process for change and test
# Rich will work on ruby so that our log entries can be included
# Kevin will work with Rich on consuming those log entries in the GUI
{column}
{column:width=40%}
{panel:title=Attendees}
* Kevin Gomes
* Brian Schlining
* Rich Schramm
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Mack.&nbsp; Blowing.&nbsp; April 20, recover Bruce.
\\

{color:#339900}April 14 Deploy NEO.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
\\
\\]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 20{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
\\
\\]]></property>
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<property name="body"><![CDATA[h3. Science Meeting

Present: Jim B., Roman, Chris P., Chris S., Bill
Absent: Julie (deployment), John (sick)

{color:#3300ff}1. Updates:{color}\\
* {color:#3300ff}Brian Schlining and image analysis{color}
** Science has met with him to discuss/explain anomolies in the comp spot intensities.
** Chris S. states that the comp spots are not reliable indicators of background as they are very sensitive to small changes in what we a.)lay down on the membrane, or b.) signal probe concentration.&nbsp; This will need much work to fine tune.&nbsp; Meanwhile, Brian has enough to continue his image analysis work, which will pay dividends for the upcoming MRI.

* {color:#3300ff}John Ryan and his paper.{color}
** This was his email:
*** a) Paper
QC and analysis of 2008 environmental data (satellite, AUV, moorings) is done.&nbsp; This provided clear results relevant to explaining / supporting
the probe array signals, comparing 2007/2008, and highlighting observing system needs & challenges.&nbsp; I am culling the results pool and producing
final figures and an outline this week, to be circulated.
b) Drifting ESP
The trajectory data from last year's drifting ESP test has been requested from Gene.&nbsp; When I get it, I'll provide the data and a simple velocity analysis to the ESP team, AUV Ops & the Rajan lab.
** Chris S. mentioned that drifter position data was also located in the headers of the CTD casts, located here:&nbsp; \\Tornado\ESP\2009_ESP_Deployments\CTD data from WF cruise\sCTD Data Deep ESP jun 09

* {color:#3300ff}Array      printing update{color}
** Last Saturday we replaced Cavro pump.&nbsp; Nilo coming in this weekend to print arrays, but his schedule is becoming busier at school.&nbsp; Roman may have to step in and help.&nbsp; Two 'spare' printer kits have been ordered and delivered.&nbsp; We estimate a need of 70 HAB arrays, and 12 (Bac arrays?) for Gordon.

* {color:#3300ff}Bruce/Mack error analysis{color}
** Roman will put data in Jim's temp box.&nbsp; Looks like Bruce had one error, but Mack errored on each run.&nbsp; Jim will work up.

* NEO deployment plan
** Depoyment on May 20 will be Roman, Julie, and a TBD.
** Must replace ball screw that came undone; use a new one from Betty, not one from GG.
** Get Brent to look at pressure-out-of-range issue
** remove incorrect reagent
** CTD driver issue.&nbsp; Will talk to Brent about approaching Bob Herlien to write drivers for the newest Seabird CTD's.]]></property>
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<property name="body"><![CDATA[# [Science Meetings]
# [Engineering Meetings]
# [ESP Manual meetings]]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]
# [Feb 16]
# Feb 23 \-\- Oceans Mtg., Portland
# [Mar 2]
# [Mar 9]
# Mar 16 \-\- Jim in S. Cal scouting.  John Ryan ran mtg.
# Mar 23
# Mar 30
# Apr 6 \-\- canceled in preparation for M0 deployment]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]]]></property>
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<property name="lastModificationDate">2011-02-03 09:16:09.707</property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites
# CVS client
# gcc
# yacc

h3. Steps to build and run
# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:{code}
cvs checkout ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This will populate the patch directory with the ruby source files without overwriting the patches.
# Now run configure.{code}
./configure
{code}
# Now run make.{code}
make
{code}
# If all goes well, ruby will have built and you can install by running this as 'root'.{code}
make install
{code}
# After that, ruby should be ready to go and if you type{code}
ruby --version
{code}
You should see something like:{code}
ruby 1.6.8-mbari7/0x4770 (2009-1-19) [i686-linux]
{code}
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
{code}]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites
# CVS client
# gcc
# yacc

h3. Steps to build and run
# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:{code}
cvs checkout ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This will populate the patch directory with the ruby source files without overwriting the patches.
# Now run configure.{code}
./configure
{code}
# Now run make.{code}
make
{code}
# If all goes well, ruby will have built and you can install by running this as 'root'.{code}
make install
{code}
# After that, ruby should be ready to go and if you type{code}
ruby --version
{code}
You should see something like:{code}
ruby 1.6.8-mbari7/0x4770 (2009-1-19) [i686-linux]
{code}
]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 15 Sep 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2015Sep08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites
# CVS client
# gcc
# yacc

h3. Steps to build and run
# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:{code}
cvs checkout ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This will populate the patch directory with the ruby source files without overwriting the patches.
# Now run configure.{code}
./configure
{code}
# Now run make.{code}
make
{code}
# If all goes well, ruby will have built and you can install by running this as 'root'.{code}
make install
{code}
# After that, ruby should be ready to go and if you type{code}
ruby --version
{code}
You should see something like:{code}
ruby 1.6.8-mbari7/0x4770 (2009-1-19) [i686-linux]
{code}
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
{code}]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites
# CVS client
# gcc
# yacc

h3. Steps to build and run
# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:{code}
cvs checkout ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This will populate the patch directory with the ruby source files without overwriting the patches.
# Now run configure.{code}
./configure
{code}
# Now run make.{code}
make
{code}
# If all goes well, ruby will have built and you can install by running this as 'root'.{code}
make install
{code}
# After that, ruby should be ready to go and if you type{code}
ruby --version
{code}
You should see something like:{code}
ruby 1.6.8-mbari7/0x4770 (2009-1-19) [i686-linux]
{code}
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
{code}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 15 Sep 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2015Sep08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# 2009 Deployments]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 15 Sep 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2015Sep08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit+\] &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker

time_increment with no digits <+> is equivalent to \+1 tic.\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond


&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 15 Sep 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2015Sep08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372518</id>
</property>
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<id name="id">8945891</id>
<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:{code}
cvs checkout ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">9405245</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 15 Sep 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2015Sep08.pdf]
# [2008 Engineering Timeline]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372517</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">9405247</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372519</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">15664037</id>
<property name="body"><![CDATA[The latest MFB manual is located in the Project Library following this path:

&nbsp;//projectlibrary/ESP/Micro Fluidic Block/Users Manual/Gen2 MFB manual
\\

Link to be added soon.]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">15631287</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">8945898</id>
<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites
# CVS client
# gcc
# yacc

h3. Steps to build and run
# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:{code}
cvs checkout ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This will populate the patch directory with the ruby source files without overwriting the patches.
# Now run configure.{code}
./configure
{code}
# Now run make.{code}
make
{code}
# If all goes well, ruby will have built and you can install by running.{code}
make install
{code}]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">8913139</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">8945895</id>
<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:{code}
cvs checkout ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This will populate the patch directory with the ruby source files without overwriting the patches.
# Now run configure.{code}
./configure
{code}
# Now run make.{code}
make
{code}
# If all goes well, ruby will have built and you can install by running.{code}
make install
{code}]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">8945896</id>
<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites
# CVS client
# gcc

h3. Steps to build and run
# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:{code}
cvs checkout ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This will populate the patch directory with the ruby source files without overwriting the patches.
# Now run configure.{code}
./configure
{code}
# Now run make.{code}
make
{code}
# If all goes well, ruby will have built and you can install by running.{code}
make install
{code}]]></property>
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<id name="id">15664063</id>
<property name="body"><![CDATA[Wanted to capture here from earlier GUI meeting discussions: ESP on-board will track and provide additional state items for things like number of pucks in a tube, capacity and current volume estimate for reagent & waste bags etc.&nbsp; These items can only really be inferred by the ESP as it is initialized and run as there is no actually sensor measuring these 'states'.&nbsp;&nbsp; ]]></property>
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</property>
</object>
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<id name="id">15664054</id>
<property name="body"><![CDATA[2-Feb-2011(weekly gui meeting). There will be a keep-alive message at some interval for the case where nothing is changing in the subscribed-to states - so the dashboard can know when coms are lost with the esp. Also, still need to resolve the 'raw units' vs. 'engineering units' question. Dashboard will need to get to engineering units somehow. Brent still wants to think this thru a bit more.


3-Feb-2011 Roman pointed out that we also need to know at the dashboard when the the esp is locked up with an error. Rich discussed briefly with Brent. While it may not strictly be 'state',&nbsp; it is important info to communicate to users via the dashboard.&nbsp; Brent suggested perhaps a second socket would have the error messages (question... how would we notify the dashboard when error condition had cleared?). ]]></property>
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<id name="id">8945868</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	&nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
\\

_time_increments_:&nbsp; Increment the current real or simulated log time.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""
\\
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit+\] &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100

time_increment = <+>digit\+		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100


alias = <=>moniker\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
\\

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit+\] &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100

time_increment = <+>digit\+		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<id name="id">8945874</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit+\] &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100

time_increment = <+>digit\+		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<id name="id">8945862</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse the it to extract the its time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records.  Their formats conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	&nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
\\

_time_increments_:&nbsp; Increment the current real or simulated log time.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.
* Will only be generated if system is operating in simulated time mode.
\\ \\

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""
\\
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records.  Their formats conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	&nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
\\

_time_increments_:&nbsp; Increment the current real or simulated log time.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.
* Will only be generated if system is operating in simulated time mode.
\\
\\

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""
\\
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[.digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[.digit+\]?	&nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34

time_increment = <+>digit*\[.digit\]?		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #Ex.&nbsp; 3.14,  .1,  12

alias = <=>moniker\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the placeholder <\> must used.

An alias without a "string" deletes the alias associated with the indicated moniker
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
\\

_time_increments_:&nbsp; Increment the current real or simulated log time.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.
* Will only be generated if system is operating in simulated time mode.
\\
\\

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""
\\
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; logTime \+= specified increment

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<property name="body"><![CDATA[{mockup:testmock|2}

h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 15 Sep 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2015Sep08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].
]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:{code}
cvs checkout ESP/gen2/software
{code}

]]></property>
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</property>
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<id name="id">11829931</id>
<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Mack.&nbsp; Blowing.&nbsp; April 20, recover Bruce.\\

{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
\\ \\]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">9405197</id>
<property name="body"><![CDATA[{mockup:testmock|2}

h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 15 Sep 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2015Sep08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

April 2, 2010.&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.


Bruce (water = 55m)
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7" ]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
# Remove areas outside the filter boundaries from the filter analysis.
#* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
#* This is important since the edge of the disk creates high intensity artifacts in the filter image.
#* !fitler_3_aoi.png!
# Apply a thresholding technique to locate spots. 
#* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
#* !fitler_3_aoi_masked.png!
#* Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.

{note:title=Segmentation isn't reliable}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{note}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
# Remove areas outside the filter boundaries from the filter analysis.
#* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
#* This is important since the edge of the disk creates high intensity artifacts in the filter image.
#* !fitler_3_aoi.png!
# Apply a thresholding technique to locate spots. 
#* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
#* ! fitler_3_aoi_masked.png!
#* Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.

{note:title=Segmentation isn't reliable}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{note}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
# Remove areas outside the filter boundaries from the filter analysis.
#* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
#* This is important since the edge of the disk creates high intensity artifacts in the filter image.
# Apply a thresholding technique to locate spots. 
#* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. !HistogramUtilitiesTest_maximumEntropySplitTest.png!
#* Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.

{note:title=Segmentation isn't reliable}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{note}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
# Remove areas outside the filter boundaries from the filter analysis.
#* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
#* This is important since the edge of the disk creates high intensity artifacts in the filter image.
#* !fitler_3_aoi.png!
# Apply a thresholding technique to locate spots. 
#* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. !HistogramUtilitiesTest_maximumEntropySplitTest.png!
#* Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.

{note:title=Segmentation isn't reliable}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{note}


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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
# Remove areas outside the filter boundaries from the filter analysis.
#* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
#* This is important since the edge of the disk creates high intensity artifacts in the filter image.
# Apply a thresholding technique to locate spots. 
#* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. !HistogramUtilitiesTest_maximumEntropySplitTest.png!
#* Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.

{note:title=Segmentation isn't reliable}
There are problems with this segmentation as it's sensitive to noise and bright images. The images below illustrate the misidentification of spots; red dots indicate where the spots were detected.

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{note}


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<property name="body"><![CDATA[h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}


h3. A. [Cawthron Planning Document]

{color:#cc00ff}March 19{color}\--ESP Sea-van leaves MBARI for Oakland

{color:#cc00ff}March 20{color} \-\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight. ]]></property>
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<property name="body"><![CDATA[h3. A. [Cawthron Planning Document]


h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand.

Schockle rubber broke March 7, causing high peak accelerations as can kept pulling taught the strength member.

Recovered {color:#0000ff}March 8{color}.
\\

h3. {color:#cc00ff}{+}Cawthron Deployment{+}{color}

{color:#cc00ff}March 19{color}\--ESP Sea-van leaves MBARI for Oakland

{color:#cc00ff}March 20{color} \-\- two cores, supply box, N2 dry shipper, and array membranes leave for air freight. ]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
# Remove areas outside the filter boundaries from the filter analysis.
#* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
#* This is important since the edge of the disk creates high intensity artifacts in the filter image.
# Apply a thresholding technique to locate spots. 
#* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. !HistogramUtilitiesTest_maximumEntropySplitTest.png!
#* Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.

{note:title=Segmentation isn't reliable}
There are problems with this segmentation as it's sensitive to noise and bright images:
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{note}


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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
# Remove areas outside the filter boundaries from the filter analysis.
#* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
#* This is important since the edge of the disk creates high intensity artifacts in the filter image.
# Apply a thresholding technique to locate spots. 
#* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. !HistogramUtilitiesTest_maximumEntropySplitTest.png!
#* Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.

{note:title=Segmentation isn't reliable}
There are problems with this segmentation as it's sensitive to noise and bright images:
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.png!
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.png!
{note}

{note:title=Segmentation isn't reliable}
There are problems with this segmentation as it's sensitive to noise and bright images:
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.png!
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.png!
{note}
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
# Remove areas outside the filter boundaries from the filter analysis.
#* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
#* This is important since the edge of the disk creates high intensity artifacts in the filter image.
# Apply a thresholding technique to locate spots. 
#* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. !HistogramUtilitiesTest_maximumEntropySplitTest.png!
#* Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.

{note:title=Segmentation isn't reliable}
There are problems with this segmentation as it's sensitive to noise and bright images:
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.png!
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.png!
{note}]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
# Remove areas outside the filter boundaries from the filter analysis.
#* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
#* This is important since the edge of the disk creates high intensity artifacts in the filter image.
# Apply a thresholding technique to locate spots. 
#* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. !HistogramUtilitiesTest_maximumEntropySplitTest.png!
#* Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
# Remove areas outside the filter boundaries from the filter analysis.
#* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
# Apply a thresholding technique to locate spots. 
#* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. !HistogramUtilitiesTest_maximumEntropySplitTest.png!]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
# Remove areas outside the filter boundaries from the filter analysis.
#* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
# Apply a thresholding technique to locate spots. 
#* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution.]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
# ]]></property>
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# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h2. Example Image

For this document I will be using this image as my filter sample:


h1. {anchor:segmentation}Segmentation

In order to identify the spots on the filter image I tried the following:
# ]]></property>
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# [Identifying spots on the filter image (_Segmentation_)|#segmentation]
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image

h1. {anchor:segmentation}Segmentation]]></property>
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# Identifying spots on the filter image (_Segmentation_)
# Extracting a single filter from the GAL file
# Aligning the GAL spots with the filter spots
# Extracting the intensities values from the filter image]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter 
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size. 
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. Automated Image Analysis.

Just isn't there yet. Notes on what's been explored can be found [here|ESP Automated Image Analysis]

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

{info:title=How is the Intensity Calculated?}
The analysis results are based on:
# the spot diameter 
#* The spot diameter defines the area that will be examined for a particular spot.
# the block size. 
#* Defines the width and height of the area to be averaged for mean intensity.
#* For example, a block size of 3 will calculate the mean for a 3 pixel by 3 pixel block.

A spot is analyzed as follows:
# The mean intensity for every _block_ (defined by block size) that fits in the circle defined by _spot diameter_ is calculated. This is done separately for each spot.
# The highest mean intensity value for a given spot is selected.
# Statistics are calculate based on the location of the selected _block_
# The location and size of the selected _block_ is overlaid onto the results image so you can view exactly which pixels the mean intensity values are calculated from.
{info}

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# [30Apr2009]]]></property>
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<property name="body"><![CDATA[April 6--Bruce at M0 for surface deployment

April 15--Mack in Sphere for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

April 29--Recover Bruce at M0

May 30--Mack in sphere connected to DWSM(dive #3)]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]
# 2008 Meeting Notes

h2. Engineering


h4. System Integration

# [Complete system tubing diagram |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/fluid%20worksheet%20MFB%2014-MAR-07.pdf]
# [Engineering Timeline]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]

h2. Science]]></property>
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<id name="id">15664252</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [Sampling Want Functional Req's] -- NEW --
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2007 Labor Usage]

h2. Engineering


h4. System Integration

# [Complete system tubing diagram |http://oceana.shore.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/fluid%20worksheet%20MFB%2014-MAR-07.pdf]
# [Engineering Timeline]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]

h4. Software

# [JIRA Bug Tracker|http://oceana.shore.mbari.org:8082]
# [GUI Component Development Pages|2G ESP GUI Project Page]

h2. Science]]></property>
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<property name="body"><![CDATA[Functional Requirements Document for D-ESP Wand*

*Rev. 1.1*

*Feb 14, 2011*\\

1.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand shall be capable of collecting a DWSM water sample and providing contextual sensor water from a point (ROV positioned) up to 10m away from the D-ESP and at a two position height; in the vent between \-30 to \-20 cm, above the vent, 20 to 30 cm above the seafloor. ROV may be used to switch positions.

2.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand shall operated at water temperatures up to 120°C. \[_121 °C is considered to be the temperature limit to life_\].

3.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand shall also be capable of collecting a DWSM sample and providing contextual sensor water from a point nearby the ESP, at an ROV positional height between 100 and 150 cm above the seafloor.

4.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand shall measure water temperature at the collection point (measurement signal routed possibly thru the CTD). Minimum temperature accuracy is ±1 °C and resolution is better than ±1 °C. Measurements shall be collected at 15 second intervals during inhalation and at 2 minute intervals all other times. Minimum calibrated temperature shall be 0 °C. Maximum calibrated temperature shall be approximately 150 °C. Measurements shall be available real-time to be displayed in the control room when the ROV is connected to the D-ESP via cable, and recorded within D-ESP for post-deployment analysis.

5.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand shall prevent particles greater than 0.5 mm in the longest dimension from entering the collection tube for DWSM. No particle exclusion is required for the contextual sensor water.

6.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand shall include sufficient cooling capacity to deliver water that does not exceed 25 °C to DWSM, the contextual sensors, and water pump.

7.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand shall deliver water to the contextual sensors at a constant flow rate (±??) between 500 and 1000 mL/min.

8.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;DWSM intake max rate shall be ½ of the wand delivery rate.

9.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand shall be flushed between sampling events so that uncontaminated water is collected and delivered to DWSM and the contextual sensors during subsequent sampling events. It would be preferable that the contextual sensors do not make measurements of contaminated water at any time and that continuous time-series are collected throughout the deployment.

10.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The wand and tubing shall be managed and protected, during deployment and recovery, to prevent damage and fouling with ROV hydraulic lines, manipulators, and/or the thrusters.]]></property>
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<property name="body"><![CDATA[# 03Jan2008]]></property>
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<property name="body"><![CDATA[Agenda for Jan 3, 2008 ESP Engineering Mtg
10:30am-12

Tech Transfer

•&nbsp;&nbsp; &nbsp;Cheri; plan for hand cold-testing/re-valving by Jan 15
•&nbsp;&nbsp; &nbsp;Status of slow-running intake on GG
ACTION: is science finished with GG? (Chris S)
ACTION: remove GG lower pressure sensor and examine (Scott)

•&nbsp;&nbsp; &nbsp;Status of manipulator hands
•&nbsp;&nbsp; &nbsp;Mike to machine 5 more finger flags (final version)
•&nbsp;&nbsp; &nbsp;Drill out pressure sensor holes in clamps
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)

•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?
ACTION: call and find out where the company is in development (Scott)

•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?
ACTION Jose adding up inventory.&nbsp; We will need enough for 2 cores and 8 MFBs and spares (at least 1 full core and enough spares for 8 MFB's\[3 dwarves, 2 R's\]).&nbsp; Tally up, look at production run, and scale up for best economy.&nbsp; Will place order early January. (Scott)

•&nbsp;&nbsp; &nbsp;Discussion of IP tech transfer w/ LLNL?
ACTION:&nbsp; Clarify IP on valve design (Chris)
ACTION:&nbsp; Need a Gantt chart of instrument usage (Jim)

•&nbsp;&nbsp; &nbsp;CMORE workshop Jan. 14-17

MFB
•&nbsp;&nbsp; &nbsp;Update on solid Phase Extraction.&nbsp; Protocol development?

ACTION:&nbsp; place order with MAXON for MFB spares (Addie)

•&nbsp;&nbsp; &nbsp;Update on PSV valve addition and connection w/ core
ACTION: Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addie will figure out how to connect ports 3, 5, 6 with no bubbles. (Addie)

•&nbsp;&nbsp; &nbsp;Report on syringe lubrication.&nbsp; Success?

ACTION:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (Scott will email)

Software

•&nbsp;&nbsp; &nbsp;Status of current Ruby version.&nbsp; Close to lock-down?
•&nbsp;&nbsp; &nbsp;Issues for Wayne:
o&nbsp;&nbsp; &nbsp;Low power CPU replacement
o&nbsp;&nbsp; &nbsp;USB camera porting from Kernel 2.4 to Kernal 2.6
o&nbsp;&nbsp; &nbsp;Improve dwarve DC servo control algorithm
o&nbsp;&nbsp; &nbsp;Improve ESP hardware simulator (Ruby)


Sphere and 4K DWSMS

•&nbsp;&nbsp; &nbsp;New order of Pucks placed?&nbsp; Charges went through Chris S?
•&nbsp;&nbsp; &nbsp;Serial numbering of pucks
ACTION: Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott)
•&nbsp;&nbsp; &nbsp;Fluid fittings from DWSM.&nbsp; Cheri using old or ordering new?
ACTION: look into need for new fluid fittings and order if necessary (Cheri)
•&nbsp;&nbsp; &nbsp;Pressure pots.&nbsp; Ordered 1 five, 1 ten?&nbsp; Worked with Cheri to make sure they'll fit enviro chamber?
ACTION: Cheri to get pressure pot sizes to figure box structure. (Cheri)

•&nbsp;&nbsp;&nbsp; Battery/power issues for spring deployments
stick with alkaline.&nbsp; Do we need more boxes?&nbsp; Need 4 boxes initially.&nbsp; Not working on low power issues.&nbsp; Must order minimum of 1 box of batteries in early 2008.

•&nbsp;&nbsp; &nbsp;4K DWSM update
o&nbsp;&nbsp; &nbsp;machining
o&nbsp;&nbsp; &nbsp;proof of concept steel housing?
•&nbsp;&nbsp; &nbsp;Progress on 1K article?

Items Pending from last meeting:

battery box
stedim bags for aqualung
Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.
Three new surface cans for 2008



Timeline (This schedule is its own page in Confluence):
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.]]></property>
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<property name="body"><![CDATA[h1. *Agenda for Jan 3, 2008 ESP Engineering Mtg*

*10:30am-12*

h3. *Tech Transfer*

•&nbsp;&nbsp; &nbsp;Cheri; plan for hand cold-testing/re-valving by Jan 15
•&nbsp;&nbsp; &nbsp;Status of slow-running intake on GG
ACTION: is science finished with GG? (Chris S)
ACTION: remove GG lower pressure sensor and examine (Scott)

•&nbsp;&nbsp; &nbsp;Status of manipulator hands
•&nbsp;&nbsp; &nbsp;Mike to machine 5 more finger flags (final version)
•&nbsp;&nbsp; &nbsp;Drill out pressure sensor holes in clamps
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)

•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?
ACTION: call and find out where the company is in development (Scott)

•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?
ACTION Jose adding up inventory.&nbsp; We will need enough for 2 cores and 8 MFBs and spares (at least 1 full core and enough spares for 8 MFB's\[3 dwarves, 2 R's\]).&nbsp; Tally up, look at production run, and scale up for best economy.&nbsp; Will place order early January. (Scott)

•&nbsp;&nbsp; &nbsp;Discussion of IP tech transfer w/ LLNL?
ACTION:&nbsp; Clarify IP on valve design (Chris)
ACTION:&nbsp; Need a Gantt chart of instrument usage (Jim)

•&nbsp;&nbsp; &nbsp;CMORE workshop Jan. 14-17

h3. *MFB*

•&nbsp;&nbsp; &nbsp;Update on solid Phase Extraction.&nbsp; Protocol development?

ACTION:&nbsp; place order with MAXON for MFB spares (Addie)

•&nbsp;&nbsp; &nbsp;Update on PSV valve addition and connection w/ core
ACTION: Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addie will figure out how to connect ports 3, 5, 6 with no bubbles. (Addie)

•&nbsp;&nbsp; &nbsp;Report on syringe lubrication.&nbsp; Success?

ACTION:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (Scott will email)

h3.*Software*

•&nbsp;&nbsp; &nbsp;Status of current Ruby version.&nbsp; Close to lock-down?
•&nbsp;&nbsp; &nbsp;Issues for Wayne:
o&nbsp;&nbsp; &nbsp;Low power CPU replacement
o&nbsp;&nbsp; &nbsp;USB camera porting from Kernel 2.4 to Kernal 2.6
o&nbsp;&nbsp; &nbsp;Improve dwarve DC servo control algorithm
o&nbsp;&nbsp; &nbsp;Improve ESP hardware simulator (Ruby)

h3.*Sphere and 4K DWSMS*

•&nbsp;&nbsp; &nbsp;New order of Pucks placed?&nbsp; Charges went through Chris S?
•&nbsp;&nbsp; &nbsp;Serial numbering of pucks
ACTION: Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott)
•&nbsp;&nbsp; &nbsp;Fluid fittings from DWSM.&nbsp; Cheri using old or ordering new?
ACTION: look into need for new fluid fittings and order if necessary (Cheri)
•&nbsp;&nbsp; &nbsp;Pressure pots.&nbsp; Ordered 1 five, 1 ten?&nbsp; Worked with Cheri to make sure they'll fit enviro chamber?
ACTION: Cheri to get pressure pot sizes to figure box structure. (Cheri)

•&nbsp;&nbsp;&nbsp; Battery/power issues for spring deployments
stick with alkaline.&nbsp; Do we need more boxes?&nbsp; Need 4 boxes initially.&nbsp; Not working on low power issues.&nbsp; Must order minimum of 1 box of batteries in early 2008.

•&nbsp;&nbsp; &nbsp;4K DWSM update
o&nbsp;&nbsp; &nbsp;machining
o&nbsp;&nbsp; &nbsp;proof of concept steel housing?
•&nbsp;&nbsp; &nbsp;Progress on 1K article?

h3.*Items Pending from last meeting:*

battery box
stedim bags for aqualung
Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.
Three new surface cans for 2008

*Timeline (This schedule is its own page in Confluence):*
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.]]></property>
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<property name="body"><![CDATA[h1. *Agenda for Jan 3, 2008 ESP Engineering Mtg*

*10:30am-12*

h3. *Tech Transfer*

•&nbsp;&nbsp; &nbsp;Cheri; plan for hand cold-testing/re-valving by Jan 15
•&nbsp;&nbsp; &nbsp;Status of slow-running intake on GG
ACTION: is science finished with GG? (Chris S)
ACTION: remove GG lower pressure sensor and examine (Scott)

•&nbsp;&nbsp; &nbsp;Status of manipulator hands
•&nbsp;&nbsp; &nbsp;Mike to machine 5 more finger flags (final version)
•&nbsp;&nbsp; &nbsp;Drill out pressure sensor holes in clamps
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)

•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?
ACTION: call and find out where the company is in development (Scott)

•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?
ACTION Jose adding up inventory.&nbsp; We will need enough for 2 cores and 8 MFBs and spares (at least 1 full core and enough spares for 8 MFB's\[3 dwarves, 2 R's\]).&nbsp; Tally up, look at production run, and scale up for best economy.&nbsp; Will place order early January. (Scott)

•&nbsp;&nbsp; &nbsp;Discussion of IP tech transfer w/ LLNL?
ACTION:&nbsp; Clarify IP on valve design (Chris)
ACTION:&nbsp; Need a Gantt chart of instrument usage (Jim)

•&nbsp;&nbsp; &nbsp;CMORE workshop Jan. 14-17;&nbsp; Issues:* roll-up core and MFB to Pacific Forum
* clean B125 lab
* clean up MFB (get rid of sleepy/medusa of wires/tubes, have a 'show' script)\\

h3. *MFB*

•&nbsp;&nbsp; &nbsp;Update on solid Phase Extraction.&nbsp; Protocol development?

ACTION:&nbsp; place order with MAXON for MFB spares (Addie)

•&nbsp;&nbsp; &nbsp;Update on PSV valve addition and connection w/ core
ACTION: Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addie will figure out how to connect ports 3, 5, 6 with no bubbles. (Addie)

•&nbsp;&nbsp; &nbsp;Report on syringe lubrication.&nbsp; Success?

ACTION:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (Scott will email)

h3. *Software*

•&nbsp;&nbsp; &nbsp;Status of current Ruby version.&nbsp; Close to lock-down?
•&nbsp;&nbsp; &nbsp;Issues for Wayne:
o&nbsp;&nbsp; &nbsp;Low power CPU replacement
o&nbsp;&nbsp; &nbsp;USB camera porting from Kernel 2.4 to Kernal 2.6
o&nbsp;&nbsp; &nbsp;Improve dwarve DC servo control algorithm
o&nbsp;&nbsp; &nbsp;Improve ESP hardware simulator (Ruby)

h3. *Sphere and 4K DWSMS*

•&nbsp;&nbsp; &nbsp;New order of Pucks placed?&nbsp; Charges went through Chris S?
•&nbsp;&nbsp; &nbsp;Serial numbering of pucks
ACTION: Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott)
•&nbsp;&nbsp; &nbsp;Fluid fittings from DWSM.&nbsp; Cheri using old or ordering new?
ACTION: look into need for new fluid fittings and order if necessary (Cheri)
•&nbsp;&nbsp; &nbsp;Pressure pots.&nbsp; Ordered 1 five, 1 ten?&nbsp; Worked with Cheri to make sure they'll fit enviro chamber?
ACTION: Cheri to get pressure pot sizes to figure box structure. (Cheri)

•&nbsp;&nbsp;&nbsp; Battery/power issues for spring deployments
stick with alkaline.&nbsp; Do we need more boxes?&nbsp; Need 4 boxes initially.&nbsp; Not working on low power issues.&nbsp; Must order minimum of 1 box of batteries in early 2008.

•&nbsp;&nbsp; &nbsp;4K DWSM update
o&nbsp;&nbsp; &nbsp;machining
o&nbsp;&nbsp; &nbsp;proof of concept steel housing?
•&nbsp;&nbsp; &nbsp;Progress on 1K article?

h3. *Items Pending from last meeting:*

battery box
stedim bags for aqualung
Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.
Three new surface cans for 2008

*Timeline (This schedule is its own page in Confluence):*
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.]]></property>
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<property name="body"><![CDATA[h1. *Agenda for Jan 3, 2008 ESP Engineering Mtg*

*10:30am-12*

h3. *Tech Transfer*

•&nbsp;&nbsp; &nbsp;Cheri; plan for hand cold-testing/re-valving by Jan 15

Bruce in chamber on Monday and running a shuffle (looped).&nbsp; It had stopped with forearm errors.&nbsp; Brent will help find when if crashed.&nbsp; Restarted shuffle on Weds, but after awhile if gets worse and worse and stops.&nbsp; Does it both in cold and at room temp.&nbsp;

ACTION: Brent will show Cheri how to read log (BRENT & CHERI)


•&nbsp;&nbsp; &nbsp;Status of slow-running intake on GG

GG's pressure sensor broken.&nbsp; Found that the clamp holes were too small, and torquing the sensors so they were wrongly calibrated. Our fix is to recalibrate when clamps are pressurized.&nbsp; Must run a sample on GG to see if it's slow on NEO.

ACTION:&nbsp; run a sample on GG to compare to NEO (Scott)


•&nbsp;&nbsp; &nbsp;Status of manipulator hands

Work still ongoing for modification of all

Have one hand but lots of calibration issues.&nbsp; Parts for other two hands still on hold until first one works.&nbsp; Mike working on valve motor mounts and gears.

Will get one hand working then build 3 more.&nbsp;

•&nbsp;&nbsp; &nbsp;Mike to machine 5 more finger flags (final version)


•&nbsp;&nbsp; &nbsp;Drill out pressure sensor holes in clamps

ACTRION: Will do this when we revalve the cores. (Scott/Cheri)
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)

Cheri discussed the design of the linkage which make the hands not move together when they close.&nbsp;

•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?

sent an email but nothing back from company...
ACTION: call and find out where the company is in development (Scott)

•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?
ACTION Jose adding up inventory.&nbsp; We will need enough for 2 cores and 8 MFBs and spares (at least 1 full core and enough spares for 8 MFB's\[3 dwarves, 2 R's\]).&nbsp; Tally up, look at production run, and scale up for best economy.&nbsp; Will place order early January. (Scott)

ACTION: check with Jose and&nbsp; Tom (Scott)


•&nbsp;&nbsp; &nbsp;Discussion of IP tech transfer w/ LLNL?
ACTION:&nbsp; Clarify IP on valve design (Chris)
ACTION:&nbsp; Need a Gantt chart of instrument usage (Jim)

•&nbsp;&nbsp; &nbsp;CMORE workshop Jan. 14-17;&nbsp; Issues:\* roll-up core and MFB to Pacific Forum
* clean B125 lab
* clean up MFB (get rid of sleepy/medusa of wires/tubes, have a 'show' script)

Will take sleepy off MFB and give to Brent and substitute with dwarf, and Addie will work on cleaning and gussing up MFB

h3. *MFB*

•&nbsp;&nbsp; &nbsp;Update on solid Phase Extraction.&nbsp; Protocol development?

ACTION:&nbsp; place order with MAXON for MFB spares (Addie)

•&nbsp;&nbsp; &nbsp;Update on PSV valve addition and connection w/ core
ACTION: Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addie will figure out how to connect ports 3, 5, 6 with no bubbles. (Addie)

•&nbsp;&nbsp; &nbsp;Report on syringe lubrication.&nbsp; Success?

ACTION:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (Scott will email)

h3. *Software*

•&nbsp;&nbsp; &nbsp;Status of current Ruby version.&nbsp; Close to lock-down?
•&nbsp;&nbsp; &nbsp;Issues for Wayne:
o&nbsp;&nbsp; &nbsp;Low power CPU replacement
o&nbsp;&nbsp; &nbsp;USB camera porting from Kernel 2.4 to Kernal 2.6
o&nbsp;&nbsp; &nbsp;Improve dwarve DC servo control algorithm
o&nbsp;&nbsp; &nbsp;Improve ESP hardware simulator (Ruby)

h3. *Sphere and 4K DWSMS*

•&nbsp;&nbsp; &nbsp;New order of Pucks placed?&nbsp; Charges went through Chris S?
•&nbsp;&nbsp; &nbsp;Serial numbering of pucks
ACTION: Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott)
•&nbsp;&nbsp; &nbsp;Fluid fittings from DWSM.&nbsp; Cheri using old or ordering new?
ACTION: look into need for new fluid fittings and order if necessary (Cheri)
•&nbsp;&nbsp; &nbsp;Pressure pots.&nbsp; Ordered 1 five, 1 ten?&nbsp; Worked with Cheri to make sure they'll fit enviro chamber?
ACTION: Cheri to get pressure pot sizes to figure box structure. (Cheri)

•&nbsp;&nbsp;&nbsp; Battery/power issues for spring deployments
stick with alkaline.&nbsp; Do we need more boxes?&nbsp; Need 4 boxes initially.&nbsp; Not working on low power issues.&nbsp; Must order minimum of 1 box of batteries in early 2008.

•&nbsp;&nbsp; &nbsp;4K DWSM update
o&nbsp;&nbsp; &nbsp;machining
o&nbsp;&nbsp; &nbsp;proof of concept steel housing?
•&nbsp;&nbsp; &nbsp;Progress on 1K article?

h3. *Items Pending from last meeting:*

battery box
stedim bags for aqualung
Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.
Three new surface cans for 2008

*Timeline (This schedule is its own page in Confluence):*
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.]]></property>
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<property name="body"><![CDATA[h1. *Agenda for Jan 3, 2008 ESP Engineering Mtg*

*10:30am-12*

h3. *Tech Transfer*

•&nbsp;&nbsp; &nbsp;Cheri; plan for hand cold-testing/re-valving by Jan 15

Bruce in chamber on Monday and running a shuffle (looped).&nbsp; It had stopped with forearm errors.&nbsp; Brent will help find when if crashed.&nbsp; Restarted shuffle on Weds, but after awhile if gets worse and worse and stops.&nbsp; Does it both in cold and at room temp.&nbsp;

ACTION: Brent will show Cheri how to read log (BRENT & CHERI)

•&nbsp;&nbsp; &nbsp;Status of slow-running intake on GG

GG's pressure sensor broken.&nbsp; Found that the clamp holes were too small, and torquing the sensors so they were wrongly calibrated. Our fix is to recalibrate when clamps are pressurized.&nbsp; Must run a sample on GG to see if it's slow on NEO.

ACTION:&nbsp; run a sample on GG to compare to NEO (Scott)

•&nbsp;&nbsp; &nbsp;Status of manipulator hands

Work still ongoing for modification of all

Have one hand but lots of calibration issues.&nbsp; Parts for other two hands still on hold until first one works.&nbsp; Mike working on valve motor mounts and gears.

Will get one hand working then build 3 more.&nbsp;

•&nbsp;&nbsp; &nbsp;Mike to machine 5 more finger flags (final version)

•&nbsp;&nbsp; &nbsp;Drill out pressure sensor holes in clamps

ACTRION: Will do this when we revalve the cores. (Scott/Cheri)
ACTION:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly (Scott)

Cheri discussed the design of the linkage which make the hands not move together when they close.&nbsp; Currently all arms are the same.

ACTION:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands (Doug) &nbsp;

•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?

sent an email but nothing back from company...
ACTION: call and find out where the company is in development (Scott)

•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?
ACTION Jose adding up inventory.&nbsp; We will need enough for 2 cores and 8 MFBs and spares (at least 1 full core and enough spares for 8 MFB's\[3 dwarves, 2 R's\]).&nbsp; Tally up, look at production run, and scale up for best economy.&nbsp; Will place order early January. (Scott)

ACTION: check with Jose and&nbsp; Tom (Scott)

•&nbsp;&nbsp; &nbsp;Discussion of IP tech transfer w/ LLNL?
ACTION:&nbsp; Clarify IP on valve design (Chris)
ACTION:&nbsp; Need a Gantt chart of instrument usage (Jim)

•&nbsp;&nbsp; &nbsp;CMORE workshop Jan. 14-17;&nbsp; Issues:\* roll-up core and MFB to Pacific Forum
* clean B125 lab
* clean up MFB (get rid of sleepy/medusa of wires/tubes, have a 'show' script)

Will take sleepy off MFB and give to Brent and substitute with dwarf, and Addie will work on cleaning and gussing up MFB

The box in the chamber; should be as near the volume of the cylinder.&nbsp; but no endcap.&nbsp; Talk to Jim S. to build it.

Connectors; have researched how to populate the lid--only one power, ethernet, console, contextual sensors (3), modem, external sampler.&nbsp; Will remove these from the 1K housing.

ACTION:&nbsp; move connectors from 1K to the test box (Doug & Cheri)
\\

h3. *MFB*

•&nbsp;&nbsp; &nbsp;Update on solid Phase Extraction.&nbsp; Protocol development?

ACTION:&nbsp; place order with MAXON for MFB spares (Addie)

Ordered.&nbsp; just need the PO approved.&nbsp; 6-8 week lead time.&nbsp;

•&nbsp;&nbsp; &nbsp;Update on PSV valve addition and connection w/ core
ACTION: Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addie will figure out how to connect ports 3, 5, 6 with no bubbles. (Addie)

•&nbsp;&nbsp; &nbsp;Report on syringe lubrication.&nbsp; Success?

Has lubed it several times, but still getting trajectory errors.&nbsp; The motor is at the edge of it's capability (moving almost TOO slowly).&nbsp; Addie has 2-3 motors with bigger gear box, 2-3 with better encoder, and 2-3 with both.

ACTION:&nbsp; will try many of these motors, then work on flipping. Must see first if you can attain high speed.&nbsp; Must get to the slow speed of 1ul/sec. (Addie)&nbsp;

ACTION:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this (Scott/Brent/Addie)

discussion of running our reagents out at LLNL to see if we can get good results.&nbsp; should dicuss with LLNL

ACTION:&nbsp; talk to Tony and get timeline on next MFB (Jim)&nbsp;

h3. *Software*

•&nbsp;&nbsp; &nbsp;Status of current Ruby version.&nbsp; Close to lock-down?

Brent has written a fix that is more efficient when bouncing between threads.&nbsp; So no garbage collection issues now.&nbsp; Was unable to recreate the error with DWSM, but found a problem with driving the I2C bus with a fast laptop--maybe something related to how quickly data is driven to the serial command bus.&nbsp;&nbsp;

Ruby interpreter is stable for this year.&nbsp; As close to 'frozen' that we'll get.&nbsp;

ACTION: Set-up sleepy board and an elmo on desk to emulate (Brent)

ACTION:&nbsp; change laptops and ARM boards and install the new Ruby interpreter (Brent)

ACTION:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] (Brent

ACTION:&nbsp; teach Cheri and Addie how to interpret the log (Brent)

ACTION:&nbsp; Work with the auto-cal code (Brent)


•&nbsp;&nbsp; &nbsp;Issues for Wayne:
o&nbsp;&nbsp; &nbsp;Low power CPU replacement
o&nbsp;&nbsp; &nbsp;USB camera porting from Kernel 2.4 to Kernel 2.6
o&nbsp;&nbsp; &nbsp;Improve dwarve DC servo control algorithm
o&nbsp;&nbsp; &nbsp;Improve ESP hardware simulator (Ruby)

Low power CPU being put off until after spring deployment.&nbsp;&nbsp; Sirus chip may work,&nbsp; but Russian company has a great sleep state DRAM board.&nbsp; From now to March, we should explore both these options.&nbsp; March we make a decision, and then bring in Wayne the help with the implementation.


h3. *Sphere and 4K DWSMS*

•&nbsp;&nbsp; &nbsp;New order of Pucks placed?&nbsp; Charges went through Chris S?
•&nbsp;&nbsp; &nbsp;Serial numbering of pucks
ACTION: Collect and inventory all pucks (Chris S to get Nilo).&nbsp; Then will send 1/2 to Mike Parker to be etched (Scott)
•&nbsp;&nbsp; &nbsp;Pressure pots.&nbsp; Ordered 1 five, 1 ten?&nbsp; Worked with Cheri to make sure they'll fit enviro chamber?

•&nbsp;&nbsp;&nbsp; Battery/power issues for spring deployments
stick with alkaline.&nbsp; Do we need more boxes?&nbsp; Need 4 boxes initially.&nbsp; Not working on low power issues.&nbsp; Must order minimum of 1 box of batteries in early 2008.

We need a total of 6 boxes for the spring deployment, and have 5.&nbsp; 4 of those 5 are D-cells.&nbsp; Two boxes will run around $4K (without batteries)


ACTION: &nbsp; Buy two boxes, populate with D-cells.&nbsp; One with lead-acid will remain lead-acid. (Scott) Jim get account # to charge.


•&nbsp;&nbsp; &nbsp;4K DWSM update
o&nbsp;&nbsp; &nbsp;machining
o&nbsp;&nbsp; &nbsp;proof of concept steel housing?
•&nbsp;&nbsp; &nbsp;Progress on 1K article?

Will not use Ti for the sampling system.&nbsp; Until we prove the aqualung works, no need to make out of Ti.&nbsp; So will make out of SS for around $8K for the housings.&nbsp; Next month we'll build up a plastic system we can run up to 100psi.

ACTION: will try and have model done by end of Jan--depends on pumps (Doug)&nbsp;\\

h3. *Items Pending from last meeting:*


Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)
Three new surface cans for 2008

ACTION: Get quote from Gene and place order (Jim)


*Timeline (This schedule is its own page in Confluence):*
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.]]></property>
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<property name="body"><![CDATA[h1. *Agenda for Jan 3, 2008 ESP Engineering Mtg*

*10:30am-12*

h3. *Tech Transfer*

•&nbsp;&nbsp; &nbsp;Cheri; plan for hand cold-testing/re-valving by Jan 15

Bruce in chamber on Monday and running a shuffle (looped).&nbsp; It had stopped with forearm errors.&nbsp; Brent will help find when/why crashed.&nbsp; Restarted shuffle on Weds, but after awhile if gets worse and worse and stops.&nbsp; Does it both in cold and at room temp.&nbsp;

{color:#ff0000}ACTION:{color} Brent will show Cheri and Addie how to read log ({color:#0000ff}Brent & Cheri & Addie{color})

•&nbsp;&nbsp; &nbsp;Status of slow-running intake on GG

GG's pressure sensor broken.&nbsp; Found that the clamp holes were too small, and installation torqued the sensors so they were wrongly calibrated. Our fix is was to recalibrate when clamps are pressurized, but this masked the&nbsp; real problem.&nbsp; Not that pressure sensor mounting holes are correct, must run a sample on GG to see if it's smilar to NEO.

{color:#ff0000}ACTION:{color}&nbsp; run a sample on GG to compare to NEO ({color:#3300ff}Scott{color})

•&nbsp;&nbsp; &nbsp;Status of manipulator hands

Have one hand but lots of calibration issues.&nbsp; Parts for other two hands still on hold until first one works.&nbsp; Mike currently working on valve motor mounts and gears.&nbsp;

{color:#ff0000}ACTION{color}:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly ({color:#0000ff}Scott{color})

Will get one hand working then build 3 more.&nbsp; Cheri discussed the design of the linkage which make the hands not move together when they close.&nbsp; Currently all arms are the same (non-ideal) design.

{color:#ff0000}ACTION{color}:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands ({color:#0000ff}Doug{color})&nbsp;

•&nbsp;&nbsp; &nbsp;Drill out pressure sensor holes in clamps

{color:#ff0000}ACTION{color}: Will do this when we revalve the cores. ({color:#0000ff}Scott/Cheri{color})

•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?
sent an email but nothing back from company...
{color:#ff0000}ACTION{color}: call and find out where the company is in development ({color:#0000ff}Scott{color})

•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?
Jose adding up inventory.&nbsp; We will need enough for 2 cores and 8 MFBs and spares (at least 1 full core and enough spares for 8 MFB's\[3 dwarves, 2 R's\]).&nbsp; Tally up, look at production run, and scale up for best economy.&nbsp; Will place order early January.

{color:#ff0000}ACTION{color}: check with Jose and&nbsp; Tom ({color:#0000ff}Scott{color})

*•&nbsp;&nbsp; &nbsp;CMORE workshop Jan. 14-17*;&nbsp;
* roll-up core and MFB to Pacific Forum

* clean B125 lab
* clean up MFB (get rid of sleepy/medusa of wires/tubes, have a 'show' script)

Will take sleepy off MFB and give to Brent and substitute with dwarf, and Addie will work on cleaning and gussing up MFB

h4. Final Tech Transfer Issues

The plastic chamber box; should be as near the volume of the cylinder as possible.&nbsp; Will not be using endcap since it doesn't fit.&nbsp; Talk to Jim S. to build the&nbsp; box.

Connectors; have researched how to populate the lid--only one power, ethernet, console, contextual sensors (3), modem, external sampler.&nbsp; Will remove these from the 1K housing.

{color:#ff0000}ACTION{color}:&nbsp; move connectors from 1K to the test box ({color:#0000ff}Doug & Cher{color}i)
\\

h3. *MFB*

* Update on solid Phase Extraction.&nbsp; Protocol development?

SPE working well now.&nbsp; Further protocol refinements will&nbsp; wait until Chris P. has submitted her paper.&nbsp;
* place order with MAXON for MFB spares (Addie)

Ordered.&nbsp; just need the PO approved.&nbsp; 6-8 week lead time.&nbsp;
* Update on PSV valve addition and connection w/ core
* &nbsp;Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addie will figure out how to connect ports 3, 5, 6 with no bubbles. (Addie).&nbsp; They have been called; waiting for response.

•&nbsp;&nbsp; &nbsp;Report on syringe lubrication.&nbsp; Success?

Has lubed it several times, but still getting trajectory errors.&nbsp; The motor is at the edge of it's capability (moving almost TOO slowly).&nbsp; Addie has 2-3 motors with bigger gear box, 2-3 with better encoder, and 2-3 with both.

{color:#ff0000}ACTION{color}:&nbsp; will try many of these motors, then work on flipping. Must get to the slow speed of 1ul/sec. ({color:#0000ff}Addie{color})&nbsp;

{color:#ff0000}ACTION{color}:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this ({color:#0000ff}Scott/Brent/Addie{color})

There was discussion of running our reagents out at LLNL to see if we can emulate their results, but with our reagents.&nbsp; Will discuss with LLNL.

{color:#ff0000}ACTION{color}:&nbsp; talk to Tony and get timeline on next MFB ({color:#0000ff}Jim{color})&nbsp;

h3. *Software*

•&nbsp;&nbsp; &nbsp;Status of current Ruby version.&nbsp; Close to lock-down?

Brent has written a fix that is more efficient when bouncing between threads.&nbsp; So no garbage collection issues now.&nbsp; Was unable to recreate the error with DWSM, but found a problem with driving the I2C bus with a fast laptop--maybe something related to how quickly data is driven to the serial command bus.&nbsp;&nbsp;

Ruby interpreter is stable for this year.&nbsp; As close to 'frozen' that we'll get.&nbsp;

{color:#ff0000}ACTION{color}: Set-up sleepy board and an elmo on desk to emulate ({color:#0000ff}Brent{color})

{color:#ff0000}ACTION{color}:&nbsp; change laptops and ARM boards and install the new Ruby interpreter ({color:#0000ff}Brent{color})

{color:#ff0000}ACTION{color}:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] ({color:#0000ff}Brent{color})

{color:#ff0000}ACTION{color}:&nbsp; Work with the auto-cal code ({color:#0000ff}Brent{color})

•&nbsp;&nbsp; &nbsp;Issues for Wayne:
o&nbsp;&nbsp; &nbsp;Low power CPU replacement
o&nbsp;&nbsp; &nbsp;USB camera porting from Kernel 2.4 to Kernel 2.6
o&nbsp;&nbsp; &nbsp;Improve dwarve DC servo control algorithm
o&nbsp;&nbsp; &nbsp;Improve ESP hardware simulator (Ruby)

Low power CPU being put off until after spring deployment.&nbsp;&nbsp; Sirus (sp?) chip may work,&nbsp; but Russian company has a great sleep state DRAM board.&nbsp; From now to March, we should explore both these options.&nbsp; March we make a decision, and then bring in Wayne the help with the implementation.

{color:#ff0000}ACTION{color}:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; ({color:#0000ff}Jim{color})&nbsp;

h3. *Sphere and 4K DWSMS*

•&nbsp;&nbsp; &nbsp;New order of Pucks placed?&nbsp; Charges went through Chris S?
•&nbsp;&nbsp; &nbsp;Serial numbering of pucks
{color:#ff0000}ACTION{color}: Collect and inventory all pucks ({color:#3300ff}Chris S to get Nilo{color}).&nbsp; Then will send 1/2 to Mike Parker to be etched ({color:#0000ff}Scott{color}).&nbsp; Still be to done.
•&nbsp;&nbsp; &nbsp;Pressure pots.&nbsp; Ordered 1 five, 1 ten.


•&nbsp;&nbsp;&nbsp; Battery/power issues for spring deployments
stick with alkaline.&nbsp; Do we need more boxes?&nbsp; Need 4 boxes initially.&nbsp; Not working on low power issues.&nbsp; Must order minimum of 1 box of batteries in early 2008.

We need a total of 6 boxes for the spring deployment, and have 5.&nbsp; 4 of those 5 are D-cells.&nbsp; Two boxes will run around $4K (without batteries)

{color:#ff0000}ACTION{color}: &nbsp; Buy two boxes, populate with D-cells.&nbsp; One with lead-acid will remain lead-acid. ({color:#0000ff}Scott) Jim{color} get account # to charge.

•&nbsp;&nbsp; &nbsp;4K DWSM update
o&nbsp;&nbsp; &nbsp;machining
o&nbsp;&nbsp; &nbsp;proof of concept steel housing?
•&nbsp;&nbsp; &nbsp;Progress on 1K article?

Will not use Ti for the sampling system.&nbsp; Until we prove the aqualung works, no need to make out of Ti.&nbsp; So will make out of SS for around $8K for the housings.&nbsp; Next month we'll build up a plastic system we can run up to 100psi.

{color:#ff0000}ACTION{color}: will try and have model done by end of Jan--depends on pumps ({color:#0000ff}Doug{color})&nbsp;
\\

h3. *Items Pending:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)
Three new surface cans for 2008

{color:#ff0000}ACTION{color}: Get quote from Gene and place order ({color:#0000ff}Jim{color})

*Timeline (This schedule is its own page in Confluence):*
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.]]></property>
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<property name="body"><![CDATA[h1. *Agenda for Jan 3, 2008 ESP Engineering Mtg*

*10:30am-12*
Present:  Jim, Cheri, Addie, Brent, Doug, Scott

h3. *Tech Transfer*

•&nbsp;&nbsp; &nbsp;Cheri; plan for hand cold-testing/re-valving by Jan 15

Bruce in chamber on Monday and running a shuffle (looped).&nbsp; It had stopped with forearm errors.&nbsp; Brent will help find when/why crashed.&nbsp; Restarted shuffle on Weds, but after awhile if gets worse and worse and stops.&nbsp; Does it both in cold and at room temp.&nbsp;

{color:#ff0000}ACTION:{color} Brent will show Cheri and Addie how to read log ({color:#0000ff}Brent & Cheri & Addie{color})

•&nbsp;&nbsp; &nbsp;Status of slow-running intake on GG

GG's pressure sensor broken.&nbsp; Found that the clamp holes were too small, and installation torqued the sensors so they were wrongly calibrated. Our fix is was to recalibrate when clamps are pressurized, but this masked the&nbsp; real problem.&nbsp; Not that pressure sensor mounting holes are correct, must run a sample on GG to see if it's smilar to NEO.

{color:#ff0000}ACTION:{color}&nbsp; run a sample on GG to compare to NEO ({color:#3300ff}Scott{color})

•&nbsp;&nbsp; &nbsp;Status of manipulator hands

Have one hand but lots of calibration issues.&nbsp; Parts for other two hands still on hold until first one works.&nbsp; Mike currently working on valve motor mounts and gears.&nbsp;

{color:#ff0000}ACTION{color}:&nbsp; meet with Mike Parker to discuss the cam assembly and redesign of the cam motor mount.&nbsp; Decide about the assembly ({color:#0000ff}Scott{color})

Will get one hand working then build 3 more.&nbsp; Cheri discussed the design of the linkage which make the hands not move together when they close.&nbsp; Currently all arms are the same (non-ideal) design.

{color:#ff0000}ACTION{color}:&nbsp; Will rev the drawing and have El Camino make enough to retrofit all hands ({color:#0000ff}Doug{color})&nbsp;

•&nbsp;&nbsp; &nbsp;Drill out pressure sensor holes in clamps

{color:#ff0000}ACTION{color}: Will do this when we revalve the cores. ({color:#0000ff}Scott/Cheri{color})

•&nbsp;&nbsp; &nbsp;Status of cold-rated syringes?
sent an email but nothing back from company...
{color:#ff0000}ACTION{color}: call and find out where the company is in development ({color:#0000ff}Scott{color})

•&nbsp;&nbsp; &nbsp;Status of Dwarf Board order?
Jose adding up inventory.&nbsp; We will need enough for 2 cores and 8 MFBs and spares (at least 1 full core and enough spares for 8 MFB's\[3 dwarves, 2 R's\]).&nbsp; Tally up, look at production run, and scale up for best economy.&nbsp; Will place order early January.

{color:#ff0000}ACTION{color}: check with Jose and&nbsp; Tom ({color:#0000ff}Scott{color})

*•&nbsp;&nbsp; &nbsp;CMORE workshop Jan. 14-17*;&nbsp;
* roll-up core and MFB to Pacific Forum

* clean B125 lab
* clean up MFB (get rid of sleepy/medusa of wires/tubes, have a 'show' script)

Will take sleepy off MFB and give to Brent and substitute with dwarf, and Addie will work on cleaning and gussing up MFB

h4. Final Tech Transfer Issues

The plastic chamber box; should be as near the volume of the cylinder as possible.&nbsp; Will not be using endcap since it doesn't fit.&nbsp; Talk to Jim S. to build the&nbsp; box.

Connectors; have researched how to populate the lid--only one power, ethernet, console, contextual sensors (3), modem, external sampler.&nbsp; Will remove these from the 1K housing.

{color:#ff0000}ACTION{color}:&nbsp; move connectors from 1K to the test box ({color:#0000ff}Doug & Cher{color}i)
\\

h3. *MFB*

* Update on solid Phase Extraction.&nbsp; Protocol development?

SPE working well now.&nbsp; Further protocol refinements will&nbsp; wait until Chris P. has submitted her paper.&nbsp;
* place order with MAXON for MFB spares (Addie)

Ordered.&nbsp; just need the PO approved.&nbsp; 6-8 week lead time.&nbsp;
* Update on PSV valve addition and connection w/ core
* &nbsp;Should talk to VICI about putting new connector in&nbsp; AIVports 3, 5, 6, to allow us to connect to 1/4-28 core fittings.&nbsp; Or see if we can use existing MFB tubing and see if compression fitting works to the 1/4-28 connections. Addie will figure out how to connect ports 3, 5, 6 with no bubbles. (Addie).&nbsp; They have been called; waiting for response.

•&nbsp;&nbsp; &nbsp;Report on syringe lubrication.&nbsp; Success?

Has lubed it several times, but still getting trajectory errors.&nbsp; The motor is at the edge of it's capability (moving almost TOO slowly).&nbsp; Addie has 2-3 motors with bigger gear box, 2-3 with better encoder, and 2-3 with both.

{color:#ff0000}ACTION{color}:&nbsp; will try many of these motors, then work on flipping. Must get to the slow speed of 1ul/sec. ({color:#0000ff}Addie{color})&nbsp;

{color:#ff0000}ACTION{color}:&nbsp; Change PSR name to ASR and change scripts. We need a naming convention for the 3-ways on the MFB.&nbsp; Brent needs to be brought in on this ({color:#0000ff}Scott/Brent/Addie{color})

There was discussion of running our reagents out at LLNL to see if we can emulate their results, but with our reagents.&nbsp; Will discuss with LLNL.

{color:#ff0000}ACTION{color}:&nbsp; talk to Tony and get timeline on next MFB ({color:#0000ff}Jim{color})&nbsp;

h3. *Software*

•&nbsp;&nbsp; &nbsp;Status of current Ruby version.&nbsp; Close to lock-down?

Brent has written a fix that is more efficient when bouncing between threads.&nbsp; So no garbage collection issues now.&nbsp; Was unable to recreate the error with DWSM, but found a problem with driving the I2C bus with a fast laptop--maybe something related to how quickly data is driven to the serial command bus.&nbsp;&nbsp;

Ruby interpreter is stable for this year.&nbsp; As close to 'frozen' that we'll get.&nbsp;

{color:#ff0000}ACTION{color}: Set-up sleepy board and an elmo on desk to emulate ({color:#0000ff}Brent{color})

{color:#ff0000}ACTION{color}:&nbsp; change laptops and ARM boards and install the new Ruby interpreter ({color:#0000ff}Brent{color})

{color:#ff0000}ACTION{color}:&nbsp; working on a cue of interrupts in the threading environment--\[low priority\] ({color:#0000ff}Brent{color})

{color:#ff0000}ACTION{color}:&nbsp; Work with the auto-cal code ({color:#0000ff}Brent{color})

•&nbsp;&nbsp; &nbsp;Issues for Wayne:
o&nbsp;&nbsp; &nbsp;Low power CPU replacement
o&nbsp;&nbsp; &nbsp;USB camera porting from Kernel 2.4 to Kernel 2.6
o&nbsp;&nbsp; &nbsp;Improve dwarve DC servo control algorithm
o&nbsp;&nbsp; &nbsp;Improve ESP hardware simulator (Ruby)

Low power CPU being put off until after spring deployment.&nbsp;&nbsp; Sirus (sp?) chip may work,&nbsp; but Russian company has a great sleep state DRAM board.&nbsp; From now to March, we should explore both these options.&nbsp; March we make a decision, and then bring in Wayne the help with the implementation.

{color:#ff0000}ACTION{color}:&nbsp; Speak with Wayne about his timeline with BIOSA and his ability to commit to low-power studies for us.&nbsp; ({color:#0000ff}Jim{color})&nbsp;

h3. *Sphere and 4K DWSMS*

•&nbsp;&nbsp; &nbsp;New order of Pucks placed?&nbsp; Charges went through Chris S?
•&nbsp;&nbsp; &nbsp;Serial numbering of pucks
{color:#ff0000}ACTION{color}: Collect and inventory all pucks ({color:#3300ff}Chris S to get Nilo{color}).&nbsp; Then will send 1/2 to Mike Parker to be etched ({color:#0000ff}Scott{color}).&nbsp; Still be to done.
•&nbsp;&nbsp; &nbsp;Pressure pots.&nbsp; Ordered 1 five, 1 ten.

•&nbsp;&nbsp;&nbsp; Battery/power issues for spring deployments
stick with alkaline.&nbsp; Do we need more boxes?&nbsp; Need 4 boxes initially.&nbsp; Not working on low power issues.&nbsp; Must order minimum of 1 box of batteries in early 2008.

We need a total of 6 boxes for the spring deployment, and have 5.&nbsp; 4 of those 5 are D-cells.&nbsp; Two boxes will run around $4K (without batteries)

{color:#ff0000}ACTION{color}: &nbsp; Buy two boxes, populate with D-cells.&nbsp; One with lead-acid will remain lead-acid. ({color:#0000ff}Scott) Jim{color} get account # to charge.

•&nbsp;&nbsp; &nbsp;4K DWSM update
o&nbsp;&nbsp; &nbsp;machining
o&nbsp;&nbsp; &nbsp;proof of concept steel housing?
•&nbsp;&nbsp; &nbsp;Progress on 1K article?

Will not use Ti for the sampling system.&nbsp; Until we prove the aqualung works, no need to make out of Ti.&nbsp; So will make out of SS for around $8K for the housings.&nbsp; Next month we'll build up a plastic system we can run up to 100psi.

{color:#ff0000}ACTION{color}: will try and have model done by end of Jan--depends on pumps ({color:#0000ff}Doug{color})&nbsp;
\\

h3. *Items Pending:*

Chris P. must work with Brent before spring deployments to solve sampling problem
Chris P. and Brent need to address high volume issues for Sept deployment.
BIOSA integration as a contextual sensor.&nbsp; ACTION: how will BIOSA integrate and drivers needed (Brent & Wayne)
Three new surface cans for 2008

{color:#ff0000}ACTION{color}: Get quote from Gene and place order ({color:#0000ff}Jim{color})

*Timeline (This schedule is its own page in Confluence):*
1.&nbsp; Cold Test Bruce with his new hand and re-valve Mack with new motors and mounts
(2 weeks; Dec 31--->Jan 15)
2. Cold test Mack w/ his new valves/hand and re-valve both Bruce and Neo (2 weeks; Jan 15-->Jan 29)
3. Begin 1 month test in chamber with MACK (~4 weeks; Feb 1-->Feb 25)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cheri to design and construct box
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Use fittings from deep canister
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * sample pressure pots
4. Prep for Spring deployments (Feb 25-->Feb 29)
5. Deploy MACK (March 3)
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Cold test Bruce (Mar 3 - Mar 17) and Neo (Mar 17 - Apr 1)
6.&nbsp; Recover MACK, Deploy BRUCE (Apr 1)
7.&nbsp; Recover BRUCE, Deploy MACK (May 1)
8. Recover MACK (May 27), Deploy both BRUCE and NEO (May 28)
9. End mission Jun 30.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Birch, Scholin, Preston, Jensen, Pargett, Roman, Demir, Ussler , Massion

h3. Items:


h4. 1.&nbsp; Drifter discussion

* Iridium Radio Checkout
** Brent has rec'd loaner phone.&nbsp; Will activate today or early next week in order to test.
** Should be returned by end of next week, unless it works for us, then we purchase ($1200/ea).&nbsp; We need 2.
** We must purchase month-to-month&nbsp; b/c prepay doesn't support short burst messaging.&nbsp; Will test open connection and SBM.
* Data logger/Controller
** We must come up with functional req's.&nbsp; Gene will set up a mtg next week with the players:&nbsp; Gene/Brent/Scott/Chris P./Hans T.
* Wave analysis is currently being performed.&nbsp; Nov waves look like they get bad very quickly.

h4. 2.&nbsp; Spring Deployment

* For adaptive sampling, we need to use nitrate and salinity.&nbsp; May add temperature but much more variable than the first two.&nbsp; Chris P. to get this data to Brent.

h4. 3.&nbsp; WHOI deployment

* &nbsp;Brent testing his comms idea and works well in lab on >200' CAT5 cable
* BUT, outside it did not.&nbsp; signal only went 50' on CAT6; 100' or more on CAT5 it did not work.
* Possible issue was radio; must retry with another radio.&nbsp; If these adapters don't work, there are more expensive German ones that will.]]></property>
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<property name="body"><![CDATA[Max temp for DWSM is 51 C (125 F). It's the tygon tubing, which can be replaced if needed. The time to replace it would be the rebuild, 3 week of Feb. PVC based tubing would have a temp rating of 73 C.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Birch, Scholin, Preston, Jensen, Pargett, Roman, Demir, Ussler , Massion


h3. Items:
\\

1.&nbsp; Drifter discussion
* Iridium Radio Checkout
** Brent has rec'd loaner phone.&nbsp; Will activate today or early next week in order to test.
** Should be returned by end of next week, unless it works for us, then we purchase ($1200/ea).&nbsp; We need 2.
** We must purchase month-to-month&nbsp; b/c prepay doesn't support short burst messaging.&nbsp; Will test open connection and SBM.
* Data logger/Controller
** We must come up with functional req's.&nbsp; Gene will set up a mtg next week with the players:&nbsp; Gene/Brent/Scott/Chris P./Hans T.
* Wave analysis is currently being performed.&nbsp; Nov waves look like they get bad very quickly.


2.&nbsp; Spring Deployment
* For adaptive sampling, we need to use nitrate and salinity.&nbsp; May add temperature but much more variable than the first two.&nbsp; Chris P. to get this data to Brent.

3.&nbsp; WHOI deployment
* &nbsp;]]></property>
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<property name="body"><![CDATA[h5. Our current (July, 2014) puck count is [here|^2014_PUCK _INVENTORYv2.xlsx|MBARI puck count].&nbsp;

Email from Scott, January 9, 2008 (updated 1-15-2008):

The current serial number format is as follows:
&nbsp;
TTTRSSS
&nbsp;
T = Type WCR (top and bottom), SHT (bottom), 1HV(top), S1V(top) LAF(top and Bottom) and, SAF(top and Bottom).
R = Revision/Lot code 0-9, A-Z
S = Serial number 000 - 999.&nbsp; This number resets at each revision, lot change.
&nbsp;
The previous Alkab run was Revision code 0.&nbsp; We had a short set of about 5 of the snap puck made by El Camino which were engraved with the R field as 1, which means that the completion set should be lot code 2.&nbsp; This is the set that Nilo is getting ready to send out now.&nbsp; When El Camino delivers the first set of 40 in March they should have lot code 3 and the remainder should be lot code 4.
&nbsp;
&nbsp;
I have started a [spreadsheet|^Puck Serial Numbers.xls] that chronicles the pucks, revisions, lots and serial numbers.
&nbsp;

{color:#ff0000}UPDATE (FEB 26, 2008){color}

&nbsp;The first half of lot code 2 was returned with some Type errors.&nbsp; Revision and Serial numbers remain unchanged, but the new Type designations will be:
\\

WCR (top and bottom)
LAF (top and bottom)
SAF (top and bottom)

SH1 (bottom)
SHT (top)

Note that we have yet to make a full batch of high-volume snap pucks, but when we do, those will be labeled 1HV (top and bottom).

Here is who is doing our etching:

LaserMark
2109 O'Toole Ave. Ste S
San Jose, CA 95131
Phone 408 433-9333
Fax 408 433-9343
\\
\\

Here is what I have packed up for etching:
| Type | Top/bottom | Numbered | Amount | NOTE |
| WCR | Top | 040-079 | 40 | \\ |
| \\ | Bottom | 040-079 | 40 | \\ |
| LAF | Top | 040-078 | 39 | 1=Missing |
| \\ | Bottom | 040-078 | 39 | 1=Missing |
| SAF | Top | 040-075 | 36 | 4sent to Gregg D |
| \\ | Bottom | 040-075 | 36 | 4sent to Gregg D |
| SHT | Top | 080-159 | 80 | \\ |
| SH1 | Bottom | 080-159 | 80 | \\ |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 390 | \\ |
\\
\\

I also sent 1 WCR puck (top&bottom) as a font sample.&nbsp; When these come back I will pack up the ones that are to be re-numbered(SHT2000-079).&nbsp; I haven't received a quote yet but Laser Mark said about $2 each piece + shipping.
\\

{color:#ff0000}UPDATE 3/24/08{color}

The SH1 tops that were misprinted are going to be sent out tomorrow to be re etched along with one of the LAF's that escaped detection last time:
| Type | Top/bottom | Numbered | Amount | NOTE |
| LAF | Top | 079 | 1 | Found the Lost 1\! |
| \\ | Bottom | 079 | 1 | \\ |
| SHT | Top | 000-079 | 80 | Old etching to be X'd out |
| \\ | \\ | \\ | \\ | \\ |
| TOTAL | \\ | \\ | 82 | \\ |
That is all for now
\\
\\
\\

{color:#ff0000}UPDATE 2/24/09&nbsp; There have been several iterations of the above serialization process since this was last updated.{color}&nbsp;

Here is where we now stand:
| This   is an inventory of pucks that have been serialized and are available for   use.&nbsp; | \\ | \\ | \\ |
| There are   aprox. 1200 more pieces (or 600 more pucks) that have yet to be serialized. | \\ | \\ |
| They are   located in the 'B' building lab | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| Type | Top/Bottom | Lot 2 | Lot 2 | Lot 3 | Lot 3 | Lot 4 | Total | \\ |
| WCR | Top | 40 | 40 | 40 | 39 | 40 | 199 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 40 | 40 | 200 | \\ |
| LAF | Top | 40 | 40 | 40 | 38 | 40 | 198 | \\ |
| \\ | Bottom | 40 | 40 | 40 | 36 | 40 | 196 | \\ |
| SAF | Top | 40 | 36 | 40 | 39 | 40 | 195 | \\ |
| \\ | Bottom | 40 | 36 | 40 | 40 | 40 | 196 | \\ |
| SHT | Top | 80 | 80 | 80 | 80 | 80 | 400 | \\ |
| SH1 \\ | Bottom | 80 | 80 | 80 | 77 | 80 | 397 | \\ |
| Total | \\ | 400 | 392 | 400 | 389 | 400 | 1981 | 990.5 |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | pieces | pucks |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| The   lot number refers to the 4th place in the serialization code:&nbsp; | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 letter type | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 1 digit lot number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | 3 digit individual part number | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| All parts   are numbered 000-079 ( except where some are missing) for each lot EXCEPT for : | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SHT=000-159 | \\ | \\ | \\ | \\ |
| \\ | \\ | \\ | \\ | SH1=000-159 | \\ | \\ | \\ | \\ |
{color:#ff0000}{*}UPDATE August 11, 2010{*}{color}

&nbsp;Puck order from McLane arrived.

Rec'd&nbsp; 160 SH1, and 80 ea of LAF, SAF, WCR, HV (consists of HV top and SH1 bottom), all laser-etched.

PO 1010318
\\

Here is their email explaining their numbering system (sent Jan 14, 2010):
{Info:title=Mclane Numbering Scheme}
{Info}
From: Tim Shanahan \[mailto:tshanahan@mclanelabs.com\]
Sent: Thursday, January 14, 2010 8:52 AM
To: 'Birch, James'
Cc: 'Pargett, Douglas'; 'Jensen, Scott'; Everlove, Cheri; 'Scholin, Chris';
Yuki Honjo (yhonjo@mclanelabs.com); Ivory Engstrom
(iengstrom@mclanelabs.com); Mike Mathewson (mathewson@mclanelabs.com)
Subject: Puck serial number format

Hello All,

We've been thinking about the serial number format for the pucks and we'd
like to suggest some modifications.&nbsp; I'm concerned about duplicating lot
numbers and the potential for having runs bigger than 1000 units.

At least for now, I think there's the possibility of McLane and MBARI still
continuing to make puck independently.&nbsp; Keeping track of the current lot
number could be problematic.

So I propose the following:

TTTMYYSSSS

TTT for type code as below.

MYY for date code in
M= 1 - 9 for Jan - Sept, A B or C for Oct Nov & Dec

YY for 2 digit year

SSSS for serial number 0000 - 9999

Also, this ensures that there never a letter I or O.

This increases the total number of characters from 7 to 10.
{info}
{info}
&nbsp;
\\
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<property name="body"><![CDATA[h4. First 'Tactical' ESP Science Users meeting
\\

Issues:

Roman


&nbsp;1.&nbsp; Comp spots still causing problems on array printing.&nbsp; Roman working on it and slowing his pace to interleave working on the instruments.

&nbsp;2.&nbsp; MOE is halfway apart/ Bruce is out of incubator.&nbsp; Both being worked on.&nbsp; Getting ready to test Bruce with chilled seawater sample.

3.&nbsp; Must start thinking of shipping to WHOI.&nbsp; New battery tube containers will not be ready.&nbsp; Using orange boxes.\\

Bill

1.&nbsp; Learning how to run the MFB.

2.&nbsp; He has his five-year review on Thursday.



Elif

1.&nbsp; Been helping out with QCing Roman's arrays. &nbsp;

2.&nbsp; Comparing new signal and capture probes

3.&nbsp; Building to cold-testing of cultures in cold seawater.\\

Chris P.

1.&nbsp; Data summary for MARS 2011 deployment is on ESPshare.

2.&nbsp; CTD and ISUS data for 2009 deployments has been given to Brent.

3.&nbsp; Pete has provided sequences and Chris may order tomorrow.

4.&nbsp; Presenting to Chavez group on Thursday RE: drifter and CANON cruise.

5.&nbsp; IPC--not needed for JdF.&nbsp; Should get it by mid-April with final batch by mid-May.&nbsp; No response from our explanation for sharing IPC outside MBARI. ]]></property>
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<property name="body"><![CDATA[h4. First 'Tactical' ESP Science Users meeting

\\

Issues:

Roman
1. Comp spots still causing problems on array printing.&nbsp; Roman working on it and slowing his pace to interleave working on the instruments.
2. MOE is halfway apart/ Bruce is out of incubator.&nbsp; Both being worked on.&nbsp; Getting ready to test Bruce with chilled seawater sample.

3. Must start thinking of shipping to WHOI. New battery tube containers will not be ready.&nbsp; Using orange boxes.
\\

Bill

1. Learning how to run the MFB.

2. He has his five-year review on Thursday.

Elif

1. Been helping out with QCing Roman's arrays. &nbsp;

2. Comparing new signal and capture probes

3. Building to cold-testing of cultures in cold seawater.
\\

Chris P.

1. Data summary for MARS 2011 deployment is on ESPshare.

2. CTD and ISUS data for 2009 deployments has been given to Brent.

3. Pete has provided sequences and Chris may order tomorrow.

4. Presenting to Chavez group on Thursday RE: drifter and CANON cruise.

5.&nbsp; IPC--not needed for JdF.&nbsp; Should get it by mid-April with final batch by mid-May.&nbsp; No response from our explanation for sharing IPC outside MBARI. ]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes (no longer maintained--Sep 2012)

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments](MB)
# [2009 Deployments](MB, MARS, SC Wharf)
# [2010 Deployments] (MB, SoCAL, Methane Mound, Drifter, MARS, SC Pier)
# [2011 Deployments](MB, GoM, Axial, Drifter-HI, SC Pier)
# [2012 Deployments] (MB, New Zealand, SoCAL, Friday Harbor, GoM, Drifter)
# [2013 Deployments] (MB, SoCAL, MARS, Puget Sound)
# [2014 Deployments] (MB, San Diego, Catalina, SoCAL, 3G)
# [2015 Deployments] (MB, SCRIPPS, 3G)
# [2016 Deployments] (3G in MB twice, SCRIPPS, Moran)
# [2017 Deployments] (3G, SCRIPPS...)
# [2018 Deployments] (3G, MB)
# [2019 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on the application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named _filter_3.tif_, will create files like _filter_3-20090430221134.png_ and _filter_3-20090430221134.txt_.

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[[G3 Process Diagrams|^G3process-04-12-12.pptx]Revised: April 12, 2012]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes (no longer maintained--Sep 2012)

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments](MB)
# [2009 Deployments](MB, MARS, SC Wharf)
# [2010 Deployments] (MB, SoCAL, Methane Mound, Drifter, MARS, SC Pier)
# [2011 Deployments](MB, GoM, Axial, Drifter-HI, SC Pier)
# [2012 Deployments] (MB, New Zealand, SoCAL, Friday Harbor, GoM, Drifter)
# [2013 Deployments] (MB, SoCAL, MARS, Puget Sound)
# [2014 Deployments] (MB, San Diego, Catalina, SoCAL, 3G)
# [2015 Deployments] (MB, SCRIPPS, 3G)
# [2016 Deployments] (3G in MB twice, SCRIPPS, Moran)
# [2017 Deployments] (3G, SCRIPPS...)
# [2018 Deployments] (3G, MB)
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[Numbering of cartridge from May, 2018 is [here|^Cartridge Numbering (24 May 2018).xlsx|3G cartridge numbering].]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http//:java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done either with directly on the image or using the sliders on application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.
Each file is named after the source file and stamped with the UTC date that the sample was analyzed.

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[h1. Cartridge part numbering

\\

Numbering of cartridge from May, 2018 is [here|^Cartridge Numbering (24 May 2018).xlsx|3G cartridge numbering].]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http::/java.com[.
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done either with directly on the image or using the sliders on application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.
Each file is named after the source file and stamped with the UTC date that the sample was analyzed.

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes (no longer maintained--Sep 2012)

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [3G Cartridge-puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments](MB)
# [2009 Deployments](MB, MARS, SC Wharf)
# [2010 Deployments] (MB, SoCAL, Methane Mound, Drifter, MARS, SC Pier)
# [2011 Deployments](MB, GoM, Axial, Drifter-HI, SC Pier)
# [2012 Deployments] (MB, New Zealand, SoCAL, Friday Harbor, GoM, Drifter)
# [2013 Deployments] (MB, SoCAL, MARS, Puget Sound)
# [2014 Deployments] (MB, San Diego, Catalina, SoCAL, 3G)
# [2015 Deployments] (MB, SCRIPPS, 3G)
# [2016 Deployments] (3G in MB twice, SCRIPPS, Moran)
# [2017 Deployments] (3G, SCRIPPS...)
# [2018 Deployments] (3G, MB)
# [2019 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes (no longer maintained--Sep 2012)

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [2G Puck Numbering System]
# [3G Cartridge-puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments](MB)
# [2009 Deployments](MB, MARS, SC Wharf)
# [2010 Deployments] (MB, SoCAL, Methane Mound, Drifter, MARS, SC Pier)
# [2011 Deployments](MB, GoM, Axial, Drifter-HI, SC Pier)
# [2012 Deployments] (MB, New Zealand, SoCAL, Friday Harbor, GoM, Drifter)
# [2013 Deployments] (MB, SoCAL, MARS, Puget Sound)
# [2014 Deployments] (MB, San Diego, Catalina, SoCAL, 3G)
# [2015 Deployments] (MB, SCRIPPS, 3G)
# [2016 Deployments] (3G in MB twice, SCRIPPS, Moran)
# [2017 Deployments] (3G, SCRIPPS...)
# [2018 Deployments] (3G, MB)
# [2019 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done either with directly on the image or using the sliders on application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.
Each file is named after the source file and stamped with the UTC date that the sample was analyzed.

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">9830800</id>
<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.
Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended.

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">9798044</id>
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<id name="id">9830799</id>
<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.
Each file is named after the source file and stamped with the UTC date that the sample was analyzed.

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">9798043</id>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">9830802</id>
<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to [http://java.com].
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done directly on the image or using the sliders on application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.

Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended.

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes (no longer maintained--Sep 2012)

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [2G Puck Numbering System]
# [3G Cartridge/puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments](MB)
# [2009 Deployments](MB, MARS, SC Wharf)
# [2010 Deployments] (MB, SoCAL, Methane Mound, Drifter, MARS, SC Pier)
# [2011 Deployments](MB, GoM, Axial, Drifter-HI, SC Pier)
# [2012 Deployments] (MB, New Zealand, SoCAL, Friday Harbor, GoM, Drifter)
# [2013 Deployments] (MB, SoCAL, MARS, Puget Sound)
# [2014 Deployments] (MB, San Diego, Catalina, SoCAL, 3G)
# [2015 Deployments] (MB, SCRIPPS, 3G)
# [2016 Deployments] (3G in MB twice, SCRIPPS, Moran)
# [2017 Deployments] (3G, SCRIPPS...)
# [2018 Deployments] (3G, MB)
# [2019 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer.
# Download the jar file to your computer.
# Double-click the jar to run the app.

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done either with directly on the image or using the sliders on application

!ESPImageMeasurement-imageControl.png!

!ESPImageMeasurement-sliderControl.png!

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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes (no longer maintained--Sep 2012)

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [3G Cartridge/puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments](MB)
# [2009 Deployments](MB, MARS, SC Wharf)
# [2010 Deployments] (MB, SoCAL, Methane Mound, Drifter, MARS, SC Pier)
# [2011 Deployments](MB, GoM, Axial, Drifter-HI, SC Pier)
# [2012 Deployments] (MB, New Zealand, SoCAL, Friday Harbor, GoM, Drifter)
# [2013 Deployments] (MB, SoCAL, MARS, Puget Sound)
# [2014 Deployments] (MB, San Diego, Catalina, SoCAL, 3G)
# [2015 Deployments] (MB, SCRIPPS, 3G)
# [2016 Deployments] (3G in MB twice, SCRIPPS, Moran)
# [2017 Deployments] (3G, SCRIPPS...)
# [2018 Deployments] (3G, MB)
# [2019 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer.
# Download the jar file to your computer.
# Double-click the jar to run the app.

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done either with directly on the image or using the sliders on application

!ESPImageMeasurement-imageControl.png!

!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.
Each file is named after the source file and stamped with the UTC date that the sample was analyzed.

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes (no longer maintained--Sep 2012)

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [3G Cartridge/puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments](MB)
# [2009 Deployments](MB, MARS, SC Wharf)
# [2010 Deployments] (MB, SoCAL, Methane Mound, Drifter, MARS, SC Pier)
# [2011 Deployments](MB, GoM, Axial, Drifter-HI, SC Pier)
# [2012 Deployments] (MB, New Zealand, SoCAL, Friday Harbor, GoM, Drifter)
# [2013 Deployments] (MB, SoCAL, MARS, Puget Sound)
# [2014 Deployments] (MB, San Diego, Catalina, SoCAL, 3G)
# [2015 Deployments] (MB, SCRIPPS, 3G)
# [2016 Deployments] (3G in MB twice, SCRIPPS, Moran)
# [2017 Deployments] (3G, SCRIPPS...)
# [2018 Deployments] (3G, MB)
# [2019 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer.
# Download the jar file to your computer.
# Double-click the jar to run the app.

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done either with directly on the image or using the sliders on application

!ESPImageMeasurement-imageControl.png!

!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.



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<property name="body"><![CDATA[h1. All dates 2011

# &nbsp;[Jan 4]
# &nbsp;[Jan 11]\\]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer.
# Download the jar file to your computer.
# Double-click the jar to run the app.

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done either with directly on the image or using the sliders on application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.
Each file is named after the source file and stamped with the UTC date that the sample was analyzed.

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer.
# [Download the jar file|http://www.mbari.org/staff/brian/software/esp-imaging-0.1-SNAPSHOT-jar-with-dependencies.jar] to your computer.
# Double-click the jar to run the app.

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done either with directly on the image or using the sliders on application

h3. Aligning using Image Controls

!ESPImageMeasurement-imageControl.png!

h3. Aligning using Slider Controls
!ESPImageMeasurement-sliderControl.png!

h2. Results

When you press the _Analyze Image_ button, 2 data products are created:
# An image with the mean intensity values overlaid
# A tab-delimited text file with intensity statistics.
Each file is named after the source file and stamped with the UTC date that the sample was analyzed.

h3. Image Result
!filter_3-20090430221134.png!

h3. Data Result
{noformat}
SpotNumber	SourceWell	Area	Mean	Median	Std	Min	Max
1	M-1	9	49355.0	48604	3539.1	43383	54869
2	M-1	9	45450.4	45237	3079.1	40195	49597
9	A-1	9	5662.1	5543	276.5	5327	6037
10	A-1	9	5863.2	5859	276.8	5451	6288
11	M-1	9	46826.3	47433	3527.7	40002	51593
12	M-1	9	41673.3	41311	5130.4	30775	47634
13	C-1	9	5684.9	5703	105.0	5530	5827
14	C-1	9	5766.2	5758	134.0	5548	6039
33	A-1	9	5564.0	5639	214.3	5294	5845
34	A-1	9	5945.6	5931	188.0	5671	6170
35	A-1	9	6444.4	6452	246.2	6127	6893
36	C-1	9	5225.2	5162	207.0	4906	5492
37	C-1	9	5627.9	5539	330.1	5185	6376
38	C-1	9	5669.4	5615	231.1	5375	6160
57	M-1	9	48217.7	47461	6614.6	35229	55771
58	M-1	9	49192.3	49033	6575.7	35924	57107
59	A-1	9	6161.3	6159	190.3	5933	6543
60	A-1	9	5979.8	6066	345.0	5545	6597
61	A-1	9	7102.6	6759	1233.1	5967	9732
62	C-1	9	5487.8	5491	100.7	5355	5626
63	C-1	9	5570.3	5510	176.3	5255	5807
64	C-1	9	5459.4	5419	133.5	5235	5641
89	M-1	9	46842.1	48813	5160.4	37888	52613
90	M-1	9	47047.8	47124	4265.9	38956	52583
91	A-1	9	6272.9	6315	439.5	5284	6872
92	A-1	9	6121.4	6141	103.7	5941	6317
93	C-1	9	5494.0	5515	174.1	5303	5767
94	C-1	9	4985.1	4965	124.4	4803	5149
113	M-1	9	48944.3	49991	3707.7	42914	53405
114	I-1	9	25423.6	25613	1422.0	22955	27031
115	I-1	9	25197.3	25670	988.3	23421	26450
116	I-1	9	22132.4	22443	1272.5	19932	23443
117	K-1	9	51498.3	51759	2560.4	47191	55187
118	K-1	9	51888.1	52335	1953.1	49773	55666
119	K-1	9	52646.9	52985	2061.7	49485	55796
120	M-1	9	30787.3	30075	3475.8	23921	35206
121	M-1	9	34149.1	33959	2733.5	29768	37348
149	M-1	9	43475.1	43663	3603.0	38100	48773
150	M-1	9	44489.3	44609	3332.0	39065	49303
151	I-1	9	23479.1	23175	1384.3	20487	25171
152	I-1	9	24453.8	24841	1268.0	22381	25655
153	I-1	9	23526.8	23690	1187.2	21538	24913
154	I-1	9	21597.7	21709	1017.7	19604	22678
155	K-1	9	49745.0	50732	2936.6	44501	52759
156	K-1	9	47913.0	48388	2031.7	43423	50437
157	K-1	9	51569.7	51321	2375.2	48169	55215
158	K-1	9	52897.6	52851	2552.0	47967	56047
189	M-1	9	47880.7	49051	2907.6	44013	53047
190	I-1	9	24703.0	24444	708.3	23487	25453
191	I-1	9	23219.3	23389	1014.5	21703	24619
192	I-1	9	21817.2	22028	1010.8	19986	23403
193	K-1	9	54369.1	54732	3718.3	46532	58461
194	K-1	9	50194.6	50399	2553.9	45703	53492
195	K-1	9	45502.8	44757	2679.8	41538	48237
196	M-1	9	26627.3	27296	2518.6	22277	28987
197	M-1	9	31814.9	32016	1982.2	28295	34746
225	M-1	9	42895.4	43709	4152.5	34537	47623
226	M-1	9	39661.4	39303	3612.6	33975	44311
227	G-1	9	5144.4	5127	221.5	4734	5587
228	G-1	9	5070.7	5139	298.5	4457	5575
229	E-1	9	4945.2	4971	133.0	4764	5193
230	E-1	9	5207.7	5205	87.9	5085	5343
249	M-1	9	41336.3	42004	2850.3	35625	45492
250	M-1	9	37665.2	38325	2081.2	34699	40801
251	G-1	9	5331.7	5387	138.8	5093	5550
252	G-1	9	5594.6	5527	147.4	5398	5792
253	G-1	9	5012.8	5011	125.8	4869	5259
254	E-1	9	5017.9	5034	129.5	4703	5139
255	E-1	9	5810.6	5767	466.6	5395	6926
256	E-1	9	5415.9	5379	171.3	5195	5705
281	G-1	9	4841.2	4835	145.3	4635	5095
282	G-1	9	5204.3	5143	146.4	5015	5403
283	G-1	9	5278.7	5249	271.8	4974	5822
284	E-1	9	5187.6	5143	135.8	5083	5519
285	E-1	9	5257.4	5282	66.5	5113	5323
286	E-1	9	4652.3	4648	151.5	4414	4918
305	G-1	9	4980.6	4964	168.7	4751	5307
306	G-1	9	4723.1	4763	82.8	4591	4804
307	M-1	9	27011.7	27094	1546.5	23564	28924
308	M-1	9	27658.3	28069	1809.2	24951	29929
309	E-1	9	4644.2	4662	80.3	4523	4731
310	E-1	9	4403.9	4429	134.1	4148	4559
329	M-1	9	33267.1	32311	3910.5	25015	36996
330	M-1	9	31966.2	33229	3090.1	26878	35366

{noformat}



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<property name="body"><![CDATA[Numbering of cartridge from May, 2018 is [here|https://oceana.mbari.org/confluence/plugins/tinymce/wysiwyg-insertlink-draft-uploadfile.action#|3G cartridge numbering].]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer.
# Download the jar file to your computer.
# Double-click the jar to run the app.

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!

h2. Alignment

When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).

Alignment can be done either with directly on the image or using the sliders on application

!ESPImageMeasurement-selection.png!

!ESPImageMeasurement-sliderControl.png!

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<property name="body"><![CDATA[h1. Before you Start

# You'll need Java 5 (or better) installed on your computer.
# Download the jar file to your computer.
# Double-click the jar to run the app.

h1. How to use it

h2. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!

h2. Selection

Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.

!ESPImageMeasurement-selection.png!]]></property>
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<property name="body"><![CDATA[h2. To run:

# You'll need Java 5 (or better) installed on your computer.
# Download the jar file to your computer.
# Double-click the jar to run the app.

h2. How to use it

h1. Setup

Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.

!ESPImageMeasurement-setup.png!]]></property>
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<property name="body"><![CDATA[[G3 Process Diagrams|^G3process-04-12-12.pptx]]]></property>
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[G3 Process Diagrams|https://oceana.mbari.org/confluence/download/attachments/18579871/G3process.pptx]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables]
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[
h2. To run:

# You'll need Java 5 (or better) installed on your computer.
# Download the jar file to your computer.
# Double-click the jar to run the app.

h2. How to use it

h1. Setup]]></property>
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<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}

{code}

h2. Extracting _Spots_ from ESP Images
]]></property>
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<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import org.mbari.esp.ia.services.ToolBox
// READ
val geneArrayIOService = ToolBox.geneArrayIOService
val galPoints = geneArrayIOService.read("https://bitbucket.org/hohonuuli/esp-image-analysis/raw/859c1f31ba5d/src/test/resources/test07/110220hab5wcomp_2011-03-07_150545_Run.txt")
// CREATE IMAGE
val bufferedImage = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 
{code}

h2. Extracting _Spots_ from ESP Images]]></property>
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<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ
val geneArrayIOService = ToolBox.geneArrayIOService
val galPoints = geneArrayIOService.read(new URL("https://bitbucket.org/hohonuuli/" +
    "esp-image-analysis/raw/859c1f31ba5d/src/test/resources/test07/" +
    "110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 
{code}

h2. Extracting _Spots_ from ESP Images]]></property>
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<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ
val geneArrayIOService = ToolBox.geneArrayIOService
val galPoints = geneArrayIOService.read(new URL("test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:


h2. Extracting _Spots_ from ESP Images]]></property>
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<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ
val geneArrayIOService = ToolBox.geneArrayIOService
val galPoints = geneArrayIOService.read(new URL("test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 100, 2)
val imageIOService = ToolBos.imageIOService
imageIOService.write(bufferedImage, new File("110220hab5wcomp_2011-03-07_150545_Run.txt"))
{code}

h2. Extracting _Spots_ from ESP Images]]></property>
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<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]

h2. Extracting _Spots_ from ESP Images

]]></property>
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<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("test07/hab11may0514h2000ml40s.tif"))

{code}]]></property>
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<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))

{code}]]></property>
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<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!]]></property>
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<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage.getProcessor).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {code}.filter(_.eccentricity()._1 < 3){code} : This snippet excludes the _least round_ spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest]]></property>
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<id name="id">19071297</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage.getProcessor).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}} : This snippet excludes the _least round_ spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038532</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071298</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage.getProcessor).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity().__1 < 3)}} : This snippet excludes the _least round_ spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038533</id>
</property>
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<id name="id">19071284</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ
val geneArrayIOService = ToolBox.geneArrayIOService
val galPoints = geneArrayIOService.read(new URL("test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Extracting _Spots_ from ESP Images]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038519</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071285</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 1000, 20)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}

h2. Extracting _Spots_ from ESP Images]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071286</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}

h2. Extracting _Spots_ from ESP Images]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071287</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h2. Extracting _Spots_ from ESP Images]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071288</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h2. Extracting _Spots_ from ESP Images]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071290</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image

h2. Extracting _Spots_ from ESP Images]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071314</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage.getProcessor).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage.getProcessor).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-spots.png!

h3. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h4. ]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071312</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage.getProcessor).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage.getProcessor).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-spots.png!]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038547</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071310</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage.getProcessor).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage.getProcessor).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
{code}
!hab11may0514h2000ml40s-with-extracted-spots.png!]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038545</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071309</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage.getProcessor).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage.getProcessor).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
{code}]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038544</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071308</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage.getProcessor).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage.getProcessor).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png")
{code}]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038543</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071307</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage.getProcessor).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import org.mbari.esp.ia.imglib.ToRGBFn
val colorImage = ToRGBFn(rawImage.getProcessor).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png")
{code}]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038542</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071306</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage.getProcessor).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import org.mbari.esp.ia.imglib.ToRGBFn
val colorImage = ToRGBFn(rawImage.getProcessor).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png")
{code}]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038541</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071305</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage.getProcessor).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import org.mbari.esp.ia.imglib.ToRGBFn
val colorImage = ToRGBFn(imagePlus.getProcessor).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png")
{code}]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038540</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071304</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage.getProcessor).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038539</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071302</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage.getProcessor).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038537</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071300</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage.getProcessor).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}} _ : This snippet excludes the _least round_ spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038535</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071299</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage.getProcessor).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}} __ This snippet excludes the _least round_ spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038534</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071329</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images

h3. The BIG Picture
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-spots.png!

h3. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h4. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h4. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn
// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutoContrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage))
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-ac-spots.png!]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038564</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071325</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images

h3. The BIG Picture
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-spots.png!

h3. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h4. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h4. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn
// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutocontrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage))
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038560</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071326</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images

h3. The BIG Picture
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-spots.png!

h3. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h4. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h4. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn
// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutoContrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage))
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038561</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071323</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-spots.png!

h3. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h4. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION of RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-raw-spots.png!]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038558</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071324</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images

h3. The BIG Picture
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-spots.png!

h3. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h4. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h4: Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn
// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutocontrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage))
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}]]></property>
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<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-spots.png!

h3. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h4. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION of RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()

{code}]]></property>
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<id name="id">15664260</id>
<property name="body"><![CDATA[[4K Sphere]]]></property>
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</property>
</object>
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<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-spots.png!

h3. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h4. First Pass: Raw Image
{code}
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION of RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawFloodFill).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()

{code}]]></property>
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<id name="id">15664259</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071317</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-spots.png!

h3. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h4. First Pass: Raw Image
{code}
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION of RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawFloodFill).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()

{code}]]></property>
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</property>
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<id name="id">19071318</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-spots.png!

h3. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h4. First Pass: Raw Image
{code}
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION of RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawFloodFill).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()

{code}]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038553</id>
</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">19071316</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif"))
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage.getProcessor).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage.getProcessor).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-spots.png!

h3. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h4. First Pass: Raw Image
{code}
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}
{code}]]></property>
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<id name="id">19071344</id>
<property name="body"><![CDATA[h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!]]></property>
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<id name="id">19071346</id>
<property name="body"><![CDATA[h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!ESP Automated Image Analysis 4^110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!ESP Automated Image Analysis 4^110220hab5wcomp_2011-03-07_150545_Run-single.png!]]></property>
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<id name="id">19071341</id>
<property name="body"><![CDATA[h2. Overview of ESP Image Analysis Automation

# [Investigations into Automated Image Analysis]]]></property>
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</property>
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<id name="id">19071338</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
{panel}
{panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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</property>
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<id name="id">19071332</id>
<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images

h3. The BIG Picture
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-spots.png!

h3. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h4. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h4. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn

// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutoContrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(acImage)).filter(_.eccentricity()._1 < 3)
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-ac-spots.png!

h4. Third Pass: Dynamic Contrast (Fuzzy-Sets)
{code}
import org.mbari.esp.ia.imglib.FuzzyContrastFn
val fuzzyContrastFn = To16BitGrayFn andThen FuzzyContrastFn
val fcImage = fuzzyContrastFn(rawImage)
val fcRegions = 
{code}]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | * Need to remove seawater <5% of lysis volume.
* In G2, remaining seawater needs to be <100uL
* Lysis volume? | * Air pressure evac (G2 method)
* Vacuum assist below filter?
* Filter holder is piston assembly, w/ small dead volumes
* Displacement with other fluid? | | 4 |
| Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | See model \\
G3LRAUVHousing.sldasm \\ | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images

h3. The BIG Picture
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-spots.png!

h3. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h4. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h4. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn

// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutoContrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(acImage)).filter(_.eccentricity()._1 < 3)
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-ac-spots.png!

h4. Third Pass: Dynamic Contrast (Fuzzy-Sets)
{code}
import org.mbari.esp.ia.imglib.FuzzyContrastFn
val fuzzyContrastFn = To16BitGrayFn andThen FuzzyContrastFn
val fcImage = fuzzyContrastFn(rawImage)
val fcRegions = SpotRegionsFn(rawImage, rawFloodFill(fcImage)).filter(_.eccentricity()._1 < 3)
val fcPoints = fcRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(fcImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = fcPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-fc-spots.png"))
g2.dispose()
{code}]]></property>
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<property name="body"><![CDATA[h2. Overview of ESP Image Analysis Automation

# [Investigations into Automated Image Analysis]
# [Extracting GAL Point Features]
# [Extracting Image Point Features]
# [Point Feature Alignment]]]></property>
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<property name="body"><![CDATA[h2. Source code

The source is hosted on at [https://bitbucket.org/hohonuuli/esp-image-analysis]. The source is written in [Scala|http://www.scala-lang.org/]

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!110220hab5wcomp_2011-03-07_150545_Run-single.png!

h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images

h3. The BIG Picture
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-spots.png!

h3. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h4. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h4. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn

// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutoContrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(acImage)).filter(_.eccentricity()._1 < 3)
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-ac-spots.png!

h4. Third Pass: Dynamic Contrast (Fuzzy-Sets)
{code}
import org.mbari.esp.ia.imglib.FuzzyContrastFn
val fuzzyContrastFn = To16BitGrayFn andThen FuzzyContrastFn
val fcImage = fuzzyContrastFn(rawImage)
val fcRegions = SpotRegionsFn(rawImage, rawFloodFill(fcImage)).filter(_.eccentricity()._1 < 3)
val fcPoints = fcRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(fcImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = fcPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-fc-spots.png"))
g2.dispose()
{code}
!hab11may0514h2000ml40s-with-extracted-fc-spots.png!]]></property>
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<property name="body"><![CDATA[h2. Overview of ESP Image Analysis Automation

# [Investigations into Automated Image Analysis]
# [Extracting GAL Information]
# [Extracting Image Point Features]
# [Point Feature Alignment]]]></property>
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<property name="body"><![CDATA[h2. Overview

In order to automate the image processing, we need to know the layout of the spots as they were defined in the original GAL file. The instructions below illustrate the steps needed to extract this information.

h1. Processing the GAL File

h2. Reading the Gene Array Layout (GAL) File

In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
{code}
import java.io.File
import java.net.URL
import org.mbari.esp.ia.services.GeneArrayAnalysisService
import org.mbari.esp.ia.services.ToolBox
// READ GAL FILE
val geneArrayIOService = ToolBox.geneArrayIOService
val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt"))
// CREATE IMAGE
val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2)
val imageIOService = ToolBox.imageIOService
imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
{code}
This produces the following image:
!ESP Automated Image Analysis 4^110220hab5wcomp_2011-03-07_150545_Run.png!

h2. Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
{code}
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image
val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500)
// CREATE IMAGE
val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10)
imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
{code}
!ESP Automated Image Analysis 4^110220hab5wcomp_2011-03-07_150545_Run-single.png!]]></property>
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<property name="body"><![CDATA[
h1. Processing an ESP Image


h2. Extracting _Spots_ from ESP Images

h3. The BIG Picture
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-spots.png!

h3. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h4. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h4. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn

// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutoContrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(acImage)).filter(_.eccentricity()._1 < 3)
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-ac-spots.png!

h4. Third Pass: Dynamic Contrast (Fuzzy-Sets)
{code}
import org.mbari.esp.ia.imglib.FuzzyContrastFn
val fuzzyContrastFn = To16BitGrayFn andThen FuzzyContrastFn
val fcImage = fuzzyContrastFn(rawImage)
val fcRegions = SpotRegionsFn(rawImage, rawFloodFill(fcImage)).filter(_.eccentricity()._1 < 3)
val fcPoints = fcRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(fcImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = fcPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-fc-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-fc-spots.png!]]></property>
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<property name="body"><![CDATA[
h2. Extracting _Spots_ from ESP Images

h1. The BIG Picture
The first step is to read the raw tiff image:
{code}
import java.net.URL
import org.mbari.esp.ia.services.ToolBox
// READ ESP TIFF IMAGE
val imageIOService = ToolBox.imageIOService
val rawImage = imageIOService.read(new URL("file:/test07/hab11may0514h2000ml40s.tif")).getProcessor
// WRITE AS PNG 
imageIOService.write(rawImage, new File("hab11may0514h2000ml40s.png"))
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s.png!

There is a small function call that extracts the image spots. Behind the scenes it does *a lot* of things. I'll start with the _big picture_ then we'll dive into the internals of how spots are extracted.
{code}
import org.mbari.esp.ia.imglib.SpotRegionsExtractorFn
val spotRegions = SpotRegionsExtractorFn(rawImage).filter(_.eccentricity()._1 < 3)
val imagePoints = spotRegions.map(_.centroid.toInt).toSeq
{code}
The above code snippet does the following:
# Extracts bright regions of the image that are most likely to represent spots of interest.
#* A region is just a collection of pixels that form a contiguous bright region
# {{filter(_.eccentricity()._1 < 3)}}  : This snippet excludes the least round spots. That is, it excludes regions that have odd shapes or ellipses as they are not likely to be spots of interest
# {{spotRegions.map(_.centroid.toInt).toSeq}} Converts each region to a point by calculating the centroid of the region. The collection of regions is converted to a {{Seq}} which is roughly equivalent to a {{java.util.List}}

We can draw the extracted points onto the image using this bit of code:
{code}
import java.io.File
import java.awt.{Color, Graphics2D}
import java.awt.geom.{Ellipse2D}
import java.awt.image.BufferedImage
import org.mbari.esp.ia.imglib.ToRGBFn

val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = imagePoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-spots.png!

h1. Under the Hood

So for simplicity, we would normally use a simple call to {{SpotRegionsExtractorFn}} to get the spots. Here's what's going on under the hood:
# Apply a contrast function
#* We make multiple passes over the rawImage applying different contrast treatments. Each treatment allows us to resolve different spots. We will walk through each treatment below.
# Threshold the image
#* This converts an image into a binary image of background (dark) areas and foreground (or bright) spots. 
# Flood fill the image
#* The flood fill applies a unique id to each contiguous foreground region. This is how we id each spot.
# Extract the spot regions

h2. First Pass: Raw Image
{code}
import ij.process.ImageProcessor
import org.mbari.esp.ia.imglib.FloodFillWithMinimumFn
import org.mbari.esp.ia.imglib.MaximumEntropyThresholdFn
import org.mbari.esp.ia.imglib.RemoveNonFilterAreaFn
import org.mbari.esp.ia.imglib.SpotRegionsFn
import org.mbari.esp.ia.imglib.To16BitGrayFn
import org.mbari.esp.ia.imglib.To8BitGrayFn

// SETUP IMAGE PROCESSING FUNCTIONS
val threshold = To8BitGrayFn andThen MaximumEntropyThresholdFn
val floodFill = {
    val floodFillWMinFn = FloodFillWithMinimumFn(5, _: ImageProcessor)
    val removeFilterFn = RemoveNonFilterAreaFn(0.75, _: ImageProcessor)
    To16BitGrayFn andThen removeFilterFn andThen floodFillWMinFn
}

// SPOT EXTRACTION OF RAW IMAGE
val rawFloodFill = threshold andThen floodFill
val rawRegions = SpotRegionsFn(rawImage, rawFloodFill(rawImage)).filter(_.eccentricity()._1 < 3)
val rawPoints = rawRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(rawImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = rawPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-raw-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-raw-spots.png!

h2. Second Pass: Autocontrasted Image
{code}
import org.mbari.esp.ia.imglib.AutoContrastFn

// SPOT EXTRACTION OF AUTOCONTRASTED IMAGE
val autoContrastFn = new AutoContrastFn(0.95)
val acImage = autoContrastFn(rawImage)
val acRegions = SpotRegionsFn(rawImage, rawFloodFill(acImage)).filter(_.eccentricity()._1 < 3)
val acPoints = acRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(acImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = acPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-ac-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-ac-spots.png!

h2. Third Pass: Dynamic Contrast (Fuzzy-Sets)
{code}
import org.mbari.esp.ia.imglib.FuzzyContrastFn
val fuzzyContrastFn = To16BitGrayFn andThen FuzzyContrastFn
val fcImage = fuzzyContrastFn(rawImage)
val fcRegions = SpotRegionsFn(rawImage, rawFloodFill(fcImage)).filter(_.eccentricity()._1 < 3)
val fcPoints = fcRegions.map(_.centroid.toInt).toSeq

// CREATE IMAGE
val colorImage = ToRGBFn(fcImage).getBufferedImage
val g2 = colorImage.getGraphics.asInstanceOf[Graphics2D]
val extractedPoints = fcPoints.map(p =>
    new Ellipse2D.Double(p.x - 2, p.y - 2, 4, 4))
g2.setPaint(Color.GREEN)
extractedPoints.foreach(g2.draw(_))
imageIOService.write(colorImage, new File("hab11may0514h2000ml40s-with-extracted-fc-spots.png"))
g2.dispose()
{code}
!ESP Automated Image Analysis 4^hab11may0514h2000ml40s-with-extracted-fc-spots.png!]]></property>
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<property name="body"><![CDATA[h2. Overview of ESP Image Analysis Automation

# [Investigations into Automated Image Analysis]
# [Extracting GAL Information]
# [Extracting Image Point Features]]]></property>
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<property name="body"><![CDATA[h2. Overview of ESP Image Analysis Automation

# [Investigations into Automated Image Analysis]
# [Extracting GAL Information]]]></property>
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<property name="body"><![CDATA[March 7, 2013


ECOHAB/CANON--So. California

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)


In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | | 2\\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[April 6--Bruce at M0 for surface deployment

April 15--Mack in Sphere for first D-ESP engineering dive\\]]></property>
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<property name="body"><![CDATA[April 6--Bruce at M0 for surface deployment

April 15--Mack in Sphere for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

April 29--Recover Bruce at M0

May 30--Mack in sphere connected to DWSM ]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://predator.shore.mbari.org/esp_gui/launch.jnlp]Project Documentation:

h3. Other Documents
# [Documents|ProjectDocuments]
# [Memos and Minutes|Project Memos Minutes]
## [Meeting with Chris, June 11, 2007]
# [Presentations|ProjectPresentations]
# [Tasks]
# [Data Model]
# [Developer Documentation]

h3. Bug Tracking
# [JIRA Issue Tracker|http://oceana.shore.mbari.org:8082/browse/ESPAPP]

]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Bill, Doug, Roman, Scott, Kevin, Jose

Absent: Scholin, Preston, Elif

h3. &nbsp;WHOI Deployment Issues

&nbsp;1.&nbsp; Discussion with Bruce K. this morning.&nbsp; He's reserved R/V Connecticut, April 17-23.&nbsp; Also has the R/V Tioga on hold.&nbsp; * Don Peters @ EOM has finished mooring design and lowered pump power req's through the gumby hose by lowering flow rate.
* They are shooting for a mid-March assembly date.
* They are ready to order Freewave modems and Brent will re-send them his suggestions.
2.&nbsp; Must talk to Theresa to begin the shipping issue.&nbsp; We will be sending ESP-Bruce, a surface mooring, and many spares (bugees, etc.)

3.&nbsp; Discussion ensued about a 'travel pack' that would allow shipment of ESP and surface mooring anywhere in the world.&nbsp; One big-ticket item is He Leak Detector; do we need a 'to-go' one?&nbsp; Consensus is we should have a leak detector; risk too high to not check.&nbsp; Doug had looked into leak detector options 1-1.5yrs ago.&nbsp; He will dig up old research.&nbsp; Perhaps we can purchase a hand-held that is better than our current one, but not as massive as the Pfeiffer.

4.&nbsp; Jose attended to get clarity on battery priorities: This was result
|| machine || Deep-ESP \\ || Bruce || MOE || ROV-Sledf ||
| Currently | 4 Lead Acid in O.Boxes \\ | &nbsp; (6 alkaline O.Boxes \\ | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ) | nothing |
| We need \\ | 8 lead acid O. Boxes \\ | 2 alkaline O. boxes \\ | 2 alkaline air-packs \\ | 8 lead-acid gels \\ |
| when? | June | April 6 \\ | April 7 \\ | June? |
129 Alkaline packs ordered (10 batteries/pack).&nbsp; Each deployment (Bruce, Moe spring, Moe Fall) will use 40 packs.

5.&nbsp; Brent has been in contact with Ivory RE: comms on the WHOI gumby.&nbsp; Ivory got 9600 baud using RS 422, but needed a ground, which was unusual.&nbsp; To make the WHOI comms work Brent estimates a week (5 full days) of work, which seems reasonable given our S. Cal experience.

6.&nbsp; Bruce is being reassembled and should be in the cold by Friday PM.

7.&nbsp; Will hold a 'travel' meeting tomorrow with Brent, Roman, and Kevin to hash out logistics of their travel to WHOI.&nbsp; Jim's office @ 11am.

h3. Jdf

1.&nbsp; Temperature probe is achilles heel.&nbsp; We've decided to go with RTD detector, and working with Scott has come up with the following design:
\\
\\

2.&nbsp; must check that CTD does switch this channel off when CTD not running.

3.&nbsp; Scott to create a parts list for this design

4.&nbsp; Bill to order variety of sheaths and RTD sensors

h4. 5.&nbsp; DWSM
# &nbsp;Gordon now out of ball
# HP interface--new pump is in--system will need a full flush
# Torque wrench found for pulling bells together for HP testing.&nbsp; Procedure is worked out.
# ISUS cans have been pressure tested and passed.&nbsp; To be handed off to Luke after they drip dry.
# New ISUS cable has arrived.
# Pulse dampers are in shop.&nbsp; Should be finished mid next week.
5.&nbsp; Travel issues:* Van gets dropped in Newport on Friday.&nbsp; We'll run the dock QC Saturday and Sunday.&nbsp; Would be easier to leave van on trailer with generator.
h3. Other:

1. Shop is slammed.&nbsp; Know this when submitting stuff.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Bill, Doug, Roman, Scott, Kevin, Jose

Absent: Scholin, Preston, Elif

h3. &nbsp;WHOI Deployment Issues

&nbsp;1.&nbsp; Discussion with Bruce K. this morning.&nbsp; He's reserved R/V Connecticut, April 17-23.&nbsp; Also has the R/V Tioga on hold.&nbsp; * Don Peters @ EOM has finished mooring design and lowered pump power req's through the gumby hose by lowering flow rate.
* They are shooting for a mid-March assembly date.
* They are ready to order Freewave modems and Brent will re-send them his suggestions.
2.&nbsp; Must talk to Theresa to begin the shipping issue.&nbsp; We will be sending ESP-Bruce, a surface mooring, and many spares (bugees, etc.)

3.&nbsp; Discussion ensued about a 'travel pack' that would allow shipment of ESP and surface mooring anywhere in the world.&nbsp; One big-ticket item is He Leak Detector; do we need a 'to-go' one?&nbsp; Consensus is we should have a leak detector; risk too high to not check.&nbsp; Doug had looked into leak detector options 1-1.5yrs ago.&nbsp; He will dig up old research.&nbsp; Perhaps we can purchase a hand-held that is better than our current one, but not as massive as the Pfeiffer.

4.&nbsp; Jose attended to get clarity on battery priorities: This was result
|| machine || Deep-ESP \\ || Bruce || MOE || ROV-Sledf ||
| Currently | 4 Lead Acid in O.Boxes \\ | &nbsp; (6 alkaline O.Boxes \\ | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ) | nothing |
| We need \\ | 8 lead acid O. Boxes \\ | 2 alkaline O. boxes \\ | 2 alkaline air-packs \\ | 8 lead-acid gels \\ |
| when? | June | April 6 \\ | April 7 \\ | June? |
129 Alkaline packs ordered (10 batteries/pack).&nbsp; Each deployment (Bruce, Moe spring, Moe Fall) will use 40 packs.

5.&nbsp; Brent has been in contact with Ivory RE: comms on the WHOI gumby.&nbsp; Ivory got 9600 baud using RS 422, but needed a ground, which was unusual.&nbsp; To make the WHOI comms work Brent estimates a week (5 full days) of work, which seems reasonable given our S. Cal experience.

6.&nbsp; Bruce is being reassembled and should be in the cold by Friday PM.

7.&nbsp; Will hold a 'travel' meeting tomorrow with Brent, Roman, and Kevin to hash out logistics of their travel to WHOI.&nbsp; Jim's office @ 11am.

h3. Jdf

1.&nbsp; Temperature probe is achilles heel.&nbsp; We've decided to go with RTD detector, and working with Scott has come up with the following design:\\ \\ \\

h3. Other:

1.&nbsp; Potential site-visit to ASU in April.&nbsp; Dates still TBD.

2.&nbsp; We will plan a PDR for G3 in Nov, 2011. ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Bill, Doug, Roman, Scott, Kevin, Jose

Absent: Scholin, Preston, Elif

h3. &nbsp;WHOI Deployment Issues

&nbsp;1.&nbsp; Discussion with Bruce K. this morning.&nbsp; He's reserved R/V Connecticut, April 17-23.&nbsp; Also has the R/V Tioga on hold.&nbsp; * Don Peters @ EOM has finished mooring design and lowered pump power req's through the gumby hose by lowering flow rate.
* They are shooting for a mid-March assembly date.
* They are ready to order Freewave modems and Brent will re-send them his suggestions.
2.&nbsp; Must talk to Theresa to begin the shipping issue.&nbsp; We will be sending ESP-Bruce, a surface mooring, and many spares (bugees, etc.)

3.&nbsp; Discussion ensued about a 'travel pack' that would allow shipment of ESP and surface mooring anywhere in the world.&nbsp; One big-ticket item is He Leak Detector; do we need a 'to-go' one?&nbsp; Consensus is we should have a leak detector; risk too high to not check.&nbsp; Doug had looked into leak detector options 1-1.5yrs ago.&nbsp; He will dig up old research.&nbsp; Perhaps we can purchase a hand-held that is better than our current one, but not as massive as the Pfeiffer.

4.&nbsp; Jose attended to get clarity on battery priorities: This was result
|| machine || Deep-ESP\\ || Bruce || MOE || ROV-Sledf ||
| Currently | 4 Lead Acid in O.Boxes\\ | &nbsp; (6 alkaline O.Boxes \\ | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ) | nothing |
| We need\\ | 8 lead acid O. Boxes\\ | 2 alkaline O. boxes\\ | 2 alkaline air-packs\\ | 8 lead-acid gels\\ |
| when? | June | April 6\\ | April 7\\ | June? |
\\

h3. Jdf

1.&nbsp; Much discussion of wand and development necessary to implement  the 'trident' structure, with temperature probes at each  intake.Conclusions:

Mechanically, building a 3-intake system is similar in difficulty to a 2-intake system.

Temperature probe design will require new development.&nbsp; 3 probes will  need data-logger, with associated wiring/cabling and pass through's.

Given the time constraints on engineering, we will develop a 2-intake  system with only 2 temperature sensors; one at vent, one at elevator.&nbsp;  Bill and Scott will look into temperature probes that will not require  separate data logger and subsequent software development.&nbsp; Roman  suggested Seabird's mini-CTD's and will ask them if they have probes  that would work for us.
2.&nbsp; We will not be implementing the wiring necessary for an ion-pump in  the ISMS for JdF.&nbsp; This development may occur for MARS in Nov, 2011.

These conclusions need to be conveyed to Pete.

3.&nbsp; Chris S. and Chris P discussed the need to develop a skeleton  mission in order to start determining the pump 'calls'.&nbsp; They wrote a  straw man on the board (Bill has copy of).&nbsp; As this matures we will fold  into the overall JdF concept of operations.

h3. Other:

1.&nbsp; Potential site-visit to ASU in April.&nbsp; Dates still TBD.

2.&nbsp; We will plan a PDR for G3 in Nov, 2011. ]]></property>
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Present:&nbsp; Jim, Brent, Bill, Doug, Roman, Scott, Kevin, Jose
Absent: Scholin, Preston, Elif

h3. &nbsp;WHOI Deployment Issues

&nbsp;1.&nbsp; Discussion with Bruce K. this morning.&nbsp; He's reserved R/V Connecticut, April 17-23.&nbsp; Also has the R/V Tioga on hold.&nbsp; * Don Peters @ EOM has finished mooring design and lowered pump power req's through the gumby hose by lowering flow rate.
* They are shooting for a mid-March assembly date.
* They are ready to order Freewave modems and Brent will re-send them his suggestions.
2.&nbsp; Must talk to Theresa to begin the shipping issue.&nbsp; We will be sending ESP-Bruce, a surface mooring, and many spares (bugees, etc.)

3.&nbsp; Discussion ensued about a 'travel pack' that would allow shipment of ESP and surface mooring anywhere in the world.&nbsp; One big-ticket item is He Leak Detector; do we need a 'to-go' one?&nbsp; Consensus is we should have a leak detector; risk too high to not check.&nbsp; Doug had looked into leak detector options 1-1.5yrs ago.&nbsp; He will dig up old research.&nbsp; Perhaps we can purchase a hand-held that is better than our current one, but not as massive as the Pfeiffer.

4.&nbsp; Jose attended to get clarity on battery priorities: This was result
|| machine || Deep-ESP \\ || Bruce || MOE || ROV-Sledf ||
| Currently | 4 Lead Acid in O.Boxes \\ | &nbsp; (6 alkaline O.Boxes \\ | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ) | nothing |
| We need \\ | 8 lead acid O. Boxes \\ | 2 alkaline O. boxes \\ | 2 alkaline air-packs \\ | 8 lead-acid gels \\ |
| when? | June | April 6 \\ | April 7 \\ | June? |
129 Alkaline packs ordered (10 batteries/pack).&nbsp; Each deployment (Bruce, Moe spring, Moe Fall) will use 40 packs.

5.&nbsp; Brent has been in contact with Ivory RE: comms on the WHOI gumby.&nbsp; Ivory got 9600 baud using RS 422, but needed a ground, which was unusual.&nbsp; To make the WHOI comms work Brent estimates a week (5 full days) of work, which seems reasonable given our S. Cal experience.

6.&nbsp; Bruce is being reassembled and should be in the cold by Friday PM.

7.&nbsp; Will hold a 'travel' meeting tomorrow with Brent, Roman, and Kevin to hash out logistics of their travel to WHOI.&nbsp; Jim's office @ 11am.

h3. Jdf

1.&nbsp; Temperature probe is achilles heel.&nbsp; We've decided to go with RTD detector, and working with Scott has come up with the following design:
\\

\\

2.&nbsp; must check that CTD does switch this channel off when CTD not running.

3.&nbsp; Scott to create a parts list for this design

4.&nbsp; Bill to order variety of sheaths and RTD sensors

h4. 5.&nbsp; DWSM

# &nbsp;Gordon now out of ball
# HP interface\--new pump is in-\-system will need a full flush
# Torque wrench found for pulling bells together for HP testing.&nbsp; Procedure is worked out.
# ISUS cans have been pressure tested and passed.&nbsp; To be handed off to Luke after they drip dry.
# New ISUS cable has arrived.
# Pulse dampers are in shop.&nbsp; Should be finished mid next week.
5.&nbsp; Travel issues:\* Van gets dropped in Newport on Friday.&nbsp; We'll run the dock QC Saturday and Sunday.&nbsp; Would be easier to leave van on trailer with generator.
h3. Other:

1. Shop is slammed.&nbsp; Know this when submitting stuff.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Bill, Doug, Roman, Scott, Kevin, Jose
Absent: Scholin, Preston, Elif

h3. &nbsp;WHOI Deployment Issues

&nbsp;1.&nbsp; Discussion with Bruce K. this morning.&nbsp; He's reserved R/V Connecticut, April 17-23.&nbsp; Also has the R/V Tioga on hold.&nbsp; * Don Peters @ EOM has finished mooring design and lowered pump power req's through the gumby hose by lowering flow rate.
* They are shooting for a mid-March assembly date.
* They are ready to order Freewave modems and Brent will re-send them his suggestions.
2.&nbsp; Must talk to Theresa to begin the shipping issue.&nbsp; We will be sending ESP-Bruce, a surface mooring, and many spares (bugees, etc.)

3.&nbsp; Discussion ensued about a 'travel pack' that would allow shipment of ESP and surface mooring anywhere in the world.&nbsp; One big-ticket item is He Leak Detector; do we need a 'to-go' one?&nbsp; Consensus is we should have a leak detector; risk too high to not check.&nbsp; Doug had looked into leak detector options 1-1.5yrs ago.&nbsp; He will dig up old research.&nbsp; Perhaps we can purchase a hand-held that is better than our current one, but not as massive as the Pfeiffer.

4.&nbsp; Jose attended to get clarity on battery priorities: This was result
|| machine || Deep-ESP \\ || Bruce || MOE || ROV-Sledf ||
| Currently | 4 Lead Acid in O.Boxes \\ | &nbsp; (6 alkaline O.Boxes \\ | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ) | nothing |
| We need \\ | 8 lead acid O. Boxes \\ | 2 alkaline O. boxes \\ | 2 alkaline air-packs \\ | 8 lead-acid gels \\ |
| when? | June | April 6 \\ | April 7 \\ | June? |
129 Alkaline packs ordered (10 batteries/pack).&nbsp; Each deployment (Bruce, Moe spring, Moe Fall) will use 40 packs.

5.&nbsp; Brent has been in contact with Ivory RE: comms on the WHOI gumby.&nbsp; Ivory got 9600 baud using RS 422, but needed a ground, which was unusual.&nbsp; To make the WHOI comms work Brent estimates a week (5 full days) of work, which seems reasonable given our S. Cal experience.

6.&nbsp; Bruce is being reassembled and should be in the cold by Friday PM.

7.&nbsp; Will hold a 'travel' meeting tomorrow with Brent, Roman, and Kevin to hash out logistics of their travel to WHOI.&nbsp; Jim's office @ 11am.

h3. Jdf

1.&nbsp; Temperature probe is achilles heel.&nbsp; We've decided to go with RTD detector, and working with Scott has come up with the following design:
\\

\\

2.&nbsp; must check that CTD does switch this channel off when CTD not running.

3.&nbsp; Scott to create a parts list for this design

4.&nbsp; Bill to order variety of sheaths and RTD sensors

h4. 5.&nbsp; DWSM

# &nbsp;Gordon now out of ball
# HP interface\--new pump is in-\-system will need a full flush
# Torque wrench found for pulling bells together for HP testing.&nbsp; Procedure is worked out.
# ISUS cans have been pressure tested and passed.&nbsp; To be handed off to Luke after they drip dry.
# New ISUS cable has arrived.
# Pulse dampers are in shop.&nbsp; Should be finished mid next week.
5.&nbsp; Travel issues:\* Van gets dropped in Newport on Friday.&nbsp; We'll run the dock QC Saturday and Sunday.&nbsp; Would be easier to leave van on trailer with generator.
h3. Other:

1. Shop is slammed.&nbsp; Know this when submitting stuff.]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Jim, Brent, Bill, Doug, Roman, Scott, Kevin, Jose
Absent: Scholin, Preston, Elif

h3. &nbsp;WHOI Deployment Issues

&nbsp;1.&nbsp; Discussion with Bruce K. this morning.&nbsp; He's reserved R/V Connecticut, April 17-23.&nbsp; Also has the R/V Tioga on hold.&nbsp; * Don Peters @ EOM has finished mooring design and lowered pump power req's through the gumby hose by lowering flow rate.
* They are shooting for a mid-March assembly date.
* They are ready to order Freewave modems and Brent will re-send them his suggestions.
2.&nbsp; Must talk to Theresa to begin the shipping issue.&nbsp; We will be sending ESP-Bruce, a surface mooring, and many spares (bugees, etc.)

3.&nbsp; Discussion ensued about a 'travel pack' that would allow shipment of ESP and surface mooring anywhere in the world.&nbsp; One big-ticket item is He Leak Detector; do we need a 'to-go' one?&nbsp; Consensus is we should have a leak detector; risk too high to not check.&nbsp; Doug had looked into leak detector options 1-1.5yrs ago.&nbsp; He will dig up old research.&nbsp; Perhaps we can purchase a hand-held that is better than our current one, but not as massive as the Pfeiffer.

4.&nbsp; Jose attended to get clarity on battery priorities: This was result
|| machine || Deep-ESP \\ || Bruce || MOE || ROV-Sledf ||
| Currently | 4 Lead Acid in O.Boxes \\ | &nbsp; (6 alkaline O.Boxes \\ | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ) | nothing |
| We need \\ | 8 lead acid O. Boxes \\ | 2 alkaline O. boxes \\ | 2 alkaline air-packs \\ | 8 lead-acid gels \\ |
| when? | June | April 6 \\ | April 7 \\ | June? |
129 Alkaline packs ordered (10 batteries/pack).&nbsp; Each deployment (Bruce, Moe spring, Moe Fall) will use 40 packs.

5.&nbsp; Brent has been in contact with Ivory RE: comms on the WHOI gumby.&nbsp; Ivory got 9600 baud using RS 422, but needed a ground, which was unusual.&nbsp; To make the WHOI comms work Brent estimates a week (5 full days) of work, which seems reasonable given our S. Cal experience.

6.&nbsp; Bruce is being reassembled and should be in the cold by Friday PM.

7.&nbsp; Will hold a 'travel' meeting tomorrow with Brent, Roman, and Kevin to hash out logistics of their travel to WHOI.&nbsp; Jim's office @ 11am.

h3. Jdf

1.&nbsp; Temperature probe is achilles heel.&nbsp; We've decided to go with RTD detector, and working with Scott has come up with the following design:
\\
{gliffy:name=probe|space=ESPAPP|page=Feb 17|pageid=15990837|align=left|size=L}
\\

2.&nbsp; must check that CTD does switch this channel off when CTD not running.

3.&nbsp; Scott to create a parts list for this design

4.&nbsp; Bill to order variety of sheaths and RTD sensors

h4. 5.&nbsp; DWSM

# &nbsp;Gordon now out of ball
# HP interface\--new pump is in-\-system will need a full flush
# Torque wrench found for pulling bells together for HP testing.&nbsp; Procedure is worked out.
# ISUS cans have been pressure tested and passed.&nbsp; To be handed off to Luke after they drip dry.
# New ISUS cable has arrived.
# Pulse dampers are in shop.&nbsp; Should be finished mid next week.
5.&nbsp; Travel issues:\* Van gets dropped in Newport on Friday.&nbsp; We'll run the dock QC Saturday and Sunday.&nbsp; Would be easier to leave van on trailer with generator.
h3. Other:

1. Shop is slammed.&nbsp; Know this when submitting stuff.]]></property>
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Present:&nbsp; Jim, Brent, Bill, Doug, Roman, Scott, Kevin, Jose

Absent: Scholin, Preston, Elif

h3. &nbsp;WHOI Deployment Issues

&nbsp;1.&nbsp; Discussion with Bruce K. this morning.&nbsp; He's reserved R/V Connecticut, April 17-23.&nbsp; Also has the R/V Tioga on hold.&nbsp; * Don Peters @ EOM has finished mooring design and lowered pump power req's through the gumby hose by lowering flow rate.
* They are shooting for a mid-March assembly date.
* They are ready to order Freewave modems and Brent will re-send them his suggestions.
2.&nbsp; Must talk to Theresa to begin the shipping issue.&nbsp; We will be sending ESP-Bruce, a surface mooring, and many spares (bugees, etc.)

3.&nbsp; Discussion ensued about a 'travel pack' that would allow shipment of ESP and surface mooring anywhere in the world.&nbsp; One big-ticket item is He Leak Detector; do we need a 'to-go' one?&nbsp; Consensus is we should have a leak detector; risk too high to not check.&nbsp; Doug had looked into leak detector options 1-1.5yrs ago.&nbsp; He will dig up old research.&nbsp; Perhaps we can purchase a hand-held that is better than our current one, but not as massive as the Pfeiffer.

4.&nbsp; Jose attended to get clarity on battery priorities: This was result
|| machine || Deep-ESP \\ || Bruce || MOE || ROV-Sledf ||
| Currently | 4 Lead Acid in O.Boxes \\ | &nbsp; (6 alkaline O.Boxes \\ | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ) | nothing |
| We need \\ | 8 lead acid O. Boxes \\ | 2 alkaline O. boxes \\ | 2 alkaline air-packs \\ | 8 lead-acid gels \\ |
| when? | June | April 6 \\ | April 7 \\ | June? |
129 Alkaline packs ordered (10 batteries/pack).&nbsp; Each deployment (Bruce, Moe spring, Moe Fall) will use 40 packs.

5.&nbsp; Brent has been in contact with Ivory RE: comms on the WHOI gumby.&nbsp; Ivory got 9600 baud using RS 422, but needed a ground, which was unusual.&nbsp; To make the WHOI comms work Brent estimates a week (5 full days) of work, which seems reasonable given our S. Cal experience.

6.&nbsp; Bruce is being reassembled and should be in the cold by Friday PM.

7.&nbsp; Will hold a 'travel' meeting tomorrow with Brent, Roman, and Kevin to hash out logistics of their travel to WHOI.&nbsp; Jim's office @ 11am.

h3. Jdf

1.&nbsp; Temperature probe is achilles heel.&nbsp; We've decided to go with RTD detector, and working with Scott has come up with the following design:
\\
\\

2.&nbsp; must check that CTD does switch this channel off when CTD not running.

3.&nbsp; Scott to create a parts list for this design

4.&nbsp; Bill to order variety of sheaths and RTD sensors

h4. 5.&nbsp; DWSM
# &nbsp;Gordon now out of ball
# HP interface--new pump is in--system will need a full flush
# Torque wrench found for pulling bells together for HP testing.&nbsp; Procedure is worked out.
# ISUS cans have been pressure tested and passed.&nbsp; To be handed off to Luke after they drip dry.
# New ISUS cable has arrived.
# Pulse dampers are in shop.&nbsp; Should be finished mid next week.
5.&nbsp; Travel issues:* Van gets dropped in Newport on Friday.&nbsp; We'll run the dock QC Saturday and Sunday.&nbsp; Would be easier to leave van on trailer with generator.
h3. Other:

1. Shop is slammed.&nbsp; Know this when submitting stuff.]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# &nbsp;[Jan 4]
# &nbsp;[Jan 11]
# [Feb 8]]]></property>
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<property name="body"><![CDATA[h4. ESP Science Users meeting

Issues:

Chris P.
# (some) probes ordered for JdF.&nbsp; Some were too clipped in the melt-curve analysis and we're waiting for new sequence from Harvard&nbsp;
# Gordon out of Ball but still with some reagents.&nbsp; Chris to run some samples collected at diffuse vent field at JdF in 2004 to see if we can get both PCR and SHA from same sample.
# Working on PCR paper.

Bill
# JdF wand design
## Spoken with Geoff Wheat who suggests getting into the vent crack.&nbsp; deeper into crack = higher temperature = more microbes. Geoff has two Antara temp probes he might loan.&nbsp; Also could get some custom HOBO's, but these wouldn't be real-time.&nbsp; Scott being consulted....
## Roman waiting to hear from Vince @ Seabird.&nbsp; They are suggesting some options, but unclear whether their temperature gauges can go hot enough.&nbsp; Currently choices are A.) Seabird, B.) interface our own probe, C.)Adam Schultz--contractor who might make us probes.&nbsp; Will work with engineering on making this decision.
## Some discussion of alternative site with hotter vents.&nbsp; Currently think that will have max of 40C at Ashes vents.
## There will be no sediment at ashes.&nbsp; It's&nbsp; ROCK.

Elif
# Ran experiment looking at array sensitivity of array when lysed from pressure pots vs. on bench.&nbsp; Both results were similar.&nbsp; This is bedrock work before going into cold temperature.&nbsp; Ultimately trying to see if cold reduces our array sensitivity; does a correction factor need to be introduced based on environmental temperature.

&nbsp;Roman
# &nbsp; Bruce being reassembled and will perform the room temp tests (full run) end of this week.&nbsp; Then into cold over weekend, and cold test early next week.
# Clamps on MOE would not compress the o-ring, so poor thermal contact on both clamps with pucks.&nbsp; Mike P looked at and found that grooves were too shallow.&nbsp; He will examine drawings and fix.&nbsp; Jim will email this issue to McLane.&nbsp;


h4. &nbsp;OTHER ISSUES:

&nbsp;Chris S. sent email to Bruce K asking what their decision was for this spring deployment.&nbsp; Still waiting to hear.

Optode:&nbsp; Two types: Clark is sensitive to oxygen, but also to H2S and needs frequent servicing.&nbsp; Optode needs far less servicing, but is less sensitive at low oxygen concentrations.&nbsp; Should we get Seabird to add an optode to one of our CTD's?&nbsp; Decision was yes, we could use both types.&nbsp; Will charge to 900915. ]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]]]></property>
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<property name="body"><![CDATA[# [Isotachophoresis]]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | See model\\
 G3LRAUVHousing.sldasm \\ | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | * Need to remove seawater <5% of lysis volume.
* In G2, remaining seawater needs to be <100uL
* Lysis volume? | * Air pressure evac (G2 method)
* Vacuum below filter
* Filter holder is piston assembly, w/ small dead volumes
*  | | 4 |
| Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | [http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand] | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | * In house design
* Lock ring to tube | See model \\
G3LRAUVHousing.sldasm \\ | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]]]></property>
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<property name="body"><![CDATA[h3. A. [Cawthron Planning Document]


h2. +Deployments during 2012 arranged chronologically+ (colors are same deployment)

\\

{color:#0000ff}March 5{color} \--&nbsp; Gordon w/PCR, CTD, and ISUS.&nbsp; Placed close to shore in shallow water (36 46.742 \-121 49.142) to test new shockle system and cell phone modem, as well as rejiggered thresholding software.&nbsp; This is system to be run in New Zealand. ]]></property>
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| G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | http://www.igus.com/wpck/default.aspx?Pagename=TwisterBand | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | | | 5 |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/\\
 Axial pull spool valve\\
 1/4 turn | 4\\ |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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<property name="body"><![CDATA[{gliffy:name=Turbine Block Diagram|space=ESPAPP|page=G3 -Turbine- Technical Options|pageid=18579908|align=left|size=L}
| G3 Function | Requirements | Technologies / Development needs \\ | Manufacturers/ \\
Collaborators \\ | Score\* |
| Ambient Flush Reservoir \\ | \\ | \\ | \\ | 1 |
| Intake point and Screen \\ | | | | 2 |
| | | | | |
| Intake Selector Valve \\
\\
Ambient Sea/Flush \\ | * 3-way valve
* 1mm min port dim
* pressure neutral
* 15 psid | * Solenoid
* oil compensated
* multi port
* flipper style
* Rocker style | \\ | 3 |
| Bulkhead valves \\ | * Isolation of seawater path
* Up to 500 psi, 1mm min port dim
* Non-corroding
* Small scale
* Low power
* Size: less than c-battery | * Direct lift solenoid valves
* Custom body valves (thread into a SAE 4 port)
* Axial flow thru valves
* Turn or axial pull valves
* Multi port valves
* Automated actuators of above valves. | | 3 |
| Cartridge Selection valves \\ | * Seawater and flush suitable
* 500 psi
* 1mm min port
* small scale
* low power
* size <AAA battery
* flush free | * Direct lift solenoid valves
* Custom body valves
* 1/4 Turn
* Axial pull
* Automated actuators of above valves.
* Multiple bank valves integrated on a manifold | * &nbsp;In house design, manifold w/ \\
Axial pull spool valve \\
1/4 turn | 4 \\ |
| Cartridge Return Array \\ | * reliable seal
* 500 psid
* <5psi opening
* any orientation
* non-corroding
* small scale | * &nbsp;spring loaded check valves
*  | * LeeCo
* Parker | 4 |
| Sea Pressure fittings/Tubing \\ | * &nbsp;500 psi
* 1mm min thru
* sea water and reagent stable
* vibration resistant
* reliable seal | * &nbsp;1/4-28 flat bottom fittings
*  | * Dibafit
* Upchurch
* LeeCo | 1 |
| Filter holder sealing \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal
* Seal validation prior to filtering | *  | | 2 |
| Filter selection valving \\
(transition form sea to reagents) \\ | * 500 psi
* sea water and reagent stable
* vibration resistant
* reliable seal | | | 4 |
| Cartridge Seals \\ | | | | 2 |
| \\ | | | | |
| \\ | \\ | \\ | | |
| Filter Media \\ | * 25mm dia (effective) area
*  | * Durapore
* Supore | \\ | 1 |
| Filter Pumping | * 75 psi (5 bar bubble point)
* Variable speed
* Max flow at least 4L/hr (@22psi)
* Min flow 300mL/hr
* Dosing accuracy <1%
* Positive displacement (or flow measuring)
* seawater suitable
* Minimal shear damage to microbes.
* Bidirectional (not required, but valuable)
* Size (with drive mech, but not motor) < soda can | * Piston pumps
* Rotating piston (Similar to DWSM)
* Syringes (with or without flow valves)
* Gear pumps (low expectation)
* Peristaltic&nbsp; (low expectation)
* Progressive cavity (typically large frame)
* Diaphragm
* Others? \\ | \\ | 3 |
| Filter Evacuate \\ | | | | 4 |
| Lyse | * Up to 1mL of buffer w/ w.o beads
* Sample particles on filter
* Qiagen Lysis buffer \\
RLT, RLT+, >RNA & DNA
* SPR buffer \\
Aq Methanol | * Bead Beating
* Heating
* Integrated heater/filter fit or holder
* Grinding
* Magnetic driven beating/grinding
* Acoustic/Sonic
* Sequential Chemistry
* Automation of the above in closed volumes
*  | DNA/RNA: \\
* (4) Microsonic (8/10 lyse) \\
w/ w.o beads
* (4) Magnet flipper
* (4) Bead Mill
* Grinder
* (2) Heat (5/10 lyse)
* Ref Bead Beat (10/10 lyse)DA/rRNA:
* (2) Heat | 4 |
| DNA/RNA purification | * Purification of 500-1000uL of lysate
* RNA and DNA in single sample desired. | * RNA and DNA extraction from one sample
* Magnetic bead \\
Need sources, size and coating
* Glass bead/fiber columns
* Non-centrifuge wash processes.
* Automated systems that perform the above. | * (3) Qiagen Membrane \\
Single use only \\
Mock up on MFB \\
May need a pressure sensor
* (4) iFast \\
May or may not be renewable \\
Currently using RLT \\
For DA: pass beads to SPR \\
For NA: no beads pass
* (3) Current silica column \\
Renewable
* (3) Chip Shop \\
Mag bead | 3 \\ |
| Direct Capture \\ | | | | |
| Reagent storage | * Bulk storage to 500mL
* Single use storage 50uL to 1mL | Blister packs \\
Prefilled syringes \\
Imbedded syringes \\
Lyophilized \\
Dry powder (beads) \\ | \\ | 4 |
| Reagent dosing | * Deliver 50-750uL doses of liquid reagent
* Deliver single shot reagent doses
* Deliver/dose powder (beads) | Compressed gas systems \\
Linear or cam actuators of blisters/syringes \\
Actuation methods for any of the above storages, such as \\
Dissolving/melting pills or isolators. \\  \\ | \\ | 4 |
| | | | | |
| Rotating Assembly \\ | * Spindle, supporting 30\+ cartridges
* Structurally supports actuator forces
* Support g loads
* Retains cartridges against g loads, pressure
* Thur bore sufficient for wiring harnesses
* Mech should sin freely, but operate \+180/-180 | * &nbsp;Cantilever spindle
* large diameter alignment bearing
* Between bearings (req's end support structure)
* Cam followers
* Additional support at actuator point. | | 2 \\ |
| Rotation Mechanism \\ | * Align cartridges to actuators
* Align cartridges to fluid transfer positions
* Accuracy: .020 at 11" dia
* Torque: drag/stiction of alignment bearings
* Specific qty of stop positions \\
or near infinite alignments?
*  | * Anti backlash
* Worm drives
* Direct gear drives
* Geneva mechanism
* No-backdrive
* DC motor,&nbsp;
* Stepper motor
* servo controller
* direct position sensing | \\ | 2 \\ |
| Flex Line/Cable Rotation Trans. \\ | * \+180/-180 motion
* maintain fitting/seals
* 2 high pressure (intake, exhaust)
* 1 low pressure (waste)
* Possibly 3\+ AM handoffs?
* Cable bundle from controls | * Snake pit, coil wrap
* torque coil | | |
| Cartridge Actuators \\ | | | | 4 |
| \\ | \\ | \\ | \\ | |
| Cartridge Waste Collector | \\ | \\ | \\ | 4 |
| Waste Storage | | * On Cartridge \\
No collector/flex lines, limited vol.
* Off Cartridge \\
Higher Vol, req collector/flex lines | | 2 |
| | | | | |
| TRANSFER TO AM | | | | |
| Cartridge to AM Selector \\ | * 90\+ ports in
* 3 ports out. | Mega-multi port valves. (90\+ ports) \\
Chip based valve to make multiport system \\
Low pressure, robotic open/seal fittings. | | 5 \\ |
| AM Selector Injection Loop \\ | | | | 4 \\ |
| Clean Injection Loop \\ | | | | 4 \\ |
| Rotor Pass-Thru \\ | | | | 2 |
| LRAUV Platform Interface \\ | | | | 2 \\ |
| LRAUV Pressure Housing \\ | * No tie rods thru housing
* Seal to tube section
* Maintain Structural support of nose/drive section | | | 5 |
| | | | | |
Scored as follows:

1: COTS components, or process, readily available, used right out of the box, without modifications.
2: New designs, with known technology and variables (no prototype testing needed, can directly design deployment hardware.)
3: OEM components, or modified COTS.
4: New prototype and designs, with known theory/physics, but unknown  technologies and variables. (prototypes need to be designed and tested  prior to deployment hardware design.)
5: New design needed, but no theory/physics are yet known that would enable the technology.]]></property>
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</property>
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<id name="id">13959181</id>
<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with Moe.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.&nbsp; {color:#ff0000}Pressure problems developed, and discovered pooched o-rings.&nbsp; MOE recovered Jun 23.{color}]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">13959180</id>
<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with Moe.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.]]></property>
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<id name="id">13959210</id>
<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]
# [May 20]
# [May 27]
# June 3
# June 10
# [June 17]]]></property>
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<id name="id">10388040</id>
<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision
# [25Jun2009]]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Wayne, Jim, Doug, Brent

Absent: Cheri, Scott, Kevin, Chris S.
\\

h3. Machine Builds

* Betty cold testing--3 issues:
*# at 2C there are borderline issues with carousel viscous friction, most definitely at \-5C.&nbsp; Inn current firmware, we can just run slower so no overcurrent.&nbsp; In new firmware we can limit PWM so there is no overcurrent (it'll just run at different speeds at diff temps)
*# Elbow misses and retrys--does it at 2C and more often at \-5C
*# Hand won't close around clmaped puck--this was the Mack issue that we've been unable to repeat

# #* &nbsp;

\*#

h3. MFB

* John Dzenitis (LLNL) is on vacation until 6-30.&nbsp; After that they will deliver 5 modules (7-6).&nbsp; Must confirm with them our total order of 12 modules with 8 spare heater elements.

h3. Drifter&nbsp;

* Drifter review this afternoon @ 1pm.

h3. Software

* Wayne taking a class at UC-B and has small class project.&nbsp; He is developing a Dwarf replacement; worried about power consumption, but looks like it may be only 20-30% higher than current dwarf, but with much more memory space.&nbsp; Wayne will talk to Scott and Brent about specifics, but class project is a go.
* Brent going to move the GUI branch onto the main branch, and then put the GUI code onto Gordon for exercise.
* Some concern as to why AIV calibration always seems to be 180degrees off.&nbsp; Brent wants to understand this and is on his to-do list.
* Syringe/sign inversion
** very difficult to duplicate in the lab so it's hard to study.&nbsp; One idea is that a bit gets set wrong that determines polarity.&nbsp; We currently don't have a way to query bit-state.&nbsp; We could take existing dwarf code and add debug ability, and it may let us see what's going on.&nbsp; Much discussion about what re-writing CPLD code and/or dwarf code might entail.&nbsp; Could be a time-sink; Scott/Brent/Wayne will get together on it.
** Discussion on whether we&nbsp; can have an error check/recovery that fixes this when it happens.&nbsp; Difficult, but Scott/Brent/Wayne to discuss.

h3. Deep ESP/DWSM

* Benthos modem issue.&nbsp; Boards ordered to replicate Hans Thomas' junction box will not work with the newer Benthos Universal Deck box.&nbsp; Jim working with Hans and Benthos to see if there is an electronic solution to problem.
* GG is going into ball to allow DWSM testing.
* Drop Wt--finished designing mechanism, and will wait on manufacture/mounting.
* Acoustic modem--not needed on MARS
* Toxicant bag--low on priority list for MARS deployment
* DWSM
** pressure transducers
*** a few will do simultaneous analog and serial output
*** must work to 2C, but most are not super cold-rated
*** Doug needs to know how we will read them.&nbsp; Talk to Scott
*** pricey ($2500/ea)
*** still getting lead times
** PISSER
*** schematic has been revised.&nbsp; Doug wants it reviewed before starts building.
** Overpressure valves
*** how will we read the contacts from the these valves?
*** will change current overpressure valves to larger ones we have on-hand.

h3. GUI

* Kevin working with Chris P to incorporate ESP parameters into GUI

h3. Deployment Issues


h3. &nbsp;Other Items]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
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<property name="body"><![CDATA[ESP team, please add to the questions:
* What will be the typical length of deployment for the Gen 3 instrument (G3)?
* What is the overall energy budget?
* Do we need our own power source or use the AUV?
* What size will the G3 be designed for?&nbsp; LRAUV size, El Dorado size, or something else?&nbsp; (*{+}maximum{+}* LRAUV payload will be 11.5" diam x 24" long)&nbsp;
* Maximum Depth
* Maximum Sampling Depth?

* What is the main function of the G3 instrument?&nbsp; Front end water processing, creating a lysate for back-end analysis?&nbsp; Or will the G3 do more than that? What?
* If simply water processing:
** how much water will be filtered?
** What will be the filtering system?&nbsp; pucks? modified pucks?&nbsp; scintered frits? something else?
** what lysate volume do you want to create?
** Will archival be necessary?

* If G3 runs assays, how many assays/tests will it be running?&nbsp; Frequency?
* Reusable assay's?
* How will decon occur?]]></property>
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<property name="body"><![CDATA[ESP team, please add to the questions:
* What will be the typical length of deployment for the Gen 3 instrument (G3)?
* What is the overall energy budget?
* Do we need our own power source or use the AUV?
* What size will the G3 be designed for?&nbsp; LRAUV size, El Dorado size, or something else?&nbsp;
* Maximum Depth
* Maximum Sampling Depth?

* What is the main function of the G3 instrument?&nbsp; Front end water processing, creating a lysate for back-end analysis?&nbsp; Or will the G3 do more than that? What?
* If simply water processing:
** how much water will be filtered?
** What will be the filtering system?&nbsp; pucks? modified pucks?&nbsp; scintered frits? something else?
** what lysate volume do you want to create?
** Will archival be necessary?

* If G3 runs assays, how many assays/tests will it be running?&nbsp; Frequency?
* Reusable assay's?
* How will decon occur?

LRAUV Payload Specs:
* 300m design depth
* Typical payload size: \~11.5" dia, 12" long
* Maximum payload size \~11.5" dia, 24" long
* Must be neutrally bouyant
* Must include presure housings and buoyancy (if needed) ]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision
# [25Jun2009]
# 02Jul2009 -- no meeting; 4th of July break
# [09Jul2009]]]></property>
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<property name="body"><![CDATA[ESP team, please add to the questions:
* What will be the typical length of deployment for the Gen 3 instrument (G3)?
* What is the overall energy budget?
* What size will the G3 be designed for?&nbsp; LRAUV size, El Dorado size, or something else?&nbsp; (*{+}maximum{+}* LRAUV payload will be 11.5" diam x 24" long)&nbsp;

* What is the main function of the G3 instrument?&nbsp; Front end water processing, creating a lysate for back-end analysis?&nbsp; Or will the G3 do more than that? What?
* If simply water processing:
** how much water will be filtered?
** What will be the filtering system?&nbsp; pucks? modified pucks?&nbsp; scintered frits? something else?
** what lysate volume do you want to create?
** Will archival be necessary?

* If G3 runs assays, how many assays/tests will it be running?&nbsp; Frequency?
* Reusable assay's?
* How will decon occur? ]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with Moe.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.&nbsp; {color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color} ]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

h4. {color:#ff00cc}Next{color}

*Set xx*]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with Moe.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.&nbsp; {color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound. ]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP\-+Mack+ w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP\-+Bruce+ w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

{color:#3300ff}{+}RECOVERY{+}{color}

*June 8, 2015*

Kevan and Roman (along with Pascal Craw) recovered North (Bruce), then South (Mack) then back to Moss Landing (2:00pm) for unload.
\\

h4. {color:#ff00cc}Next{color}

*Set xx*]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with Moe.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}
{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound. ]]></property>
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<property name="body"><![CDATA[h4. (as of April, 2015)


h1. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

*21.5m (BAD)*
Now with bad connector...&nbsp;
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos here\[^Image 2.jpg] and\[here^Image 3.jpg\].

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)

*15.2m (BAD; bad BSR?)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]

(shockles 1-4 used in SoCal ECOHAB-2013 and Monterey Bay ECOHAB-2013, but unclear which used when )

h4. ESP-001

* 44 days during Catalina (April 2014) deployment
* Moran MB deployment (Sep/Oct 2014)

h4. ESP-002

\\

h4. ESP-003

* &nbsp;32 days S. Cal ECOHAB w/Mack (Apr 2014)

h4. ESP-004

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).

h4. ESP-005


h1. Anchor lines

\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4.


h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\
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<property name="body"><![CDATA[h4. (as of April, 2015)


h1. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

*21.5m (BAD)*
Now with bad connector...&nbsp;
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos [here\^Image 2.jpg] and\[here\^Image 3.jpg].

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)

*15.2m (BAD; bad BSR?)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]

(shockles 1-4 used in SoCal ECOHAB-2013 and Monterey Bay ECOHAB-2013, but unclear which used when )

h4. ESP-001

* 44 days during Catalina (April 2014) deployment
* Moran MB deployment (Sep/Oct 2014)

h4. ESP-002

\\

h4. ESP-003

* &nbsp;32 days S. Cal ECOHAB w/Mack (Apr 2014)

h4. ESP-004

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).

h4. ESP-005


h1. Anchor lines

\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4.


h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\
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<property name="body"><![CDATA[h4. (as of April, 2015)


h1. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

{color:#ff0000}{*}21.5m (BAD)*{color}
{color:#ff0000}Now with bad connector...{color}
* {color:#ff0000}Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos{color} {color:#ff0000}[{color:#ff0000}here{color}|^Image 2.jpg|crystals]{color} {color:#ff0000}and{color} {color:#ff0000}[{color:#ff0000}here{color}|^Image 3.jpg|inside]{color}.

{color:}{*}15.6m{*}{color}
{color:}\* 35 days S. Cal ECOHAB w/Mack (Mar 2013){color}
{color:}\* 41 days MB ECOHAB w/Mack (Sep 2013){color}
{color:}\* 32 days S. Cal ECOHAB w/Mack (Apr 2014){color}

{color:}{*}15.2m (BAD; bad BSR?)*{color}
* {color:#ff0000}41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;{color}

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]

(shockles 1-4 used in SoCal ECOHAB-2013 and Monterey Bay ECOHAB-2013, but unclear which used when )

h4. ESP-001

* 44 days during Catalina (April 2014) deployment
* Moran MB deployment (Sep/Oct 2014)

h4. ESP-002

\\

h4. ESP-003

* &nbsp;32 days S. Cal ECOHAB w/Mack (Apr 2014)

h4. ESP-004

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).

h4. ESP-005


h1. Anchor lines

\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4.


h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\
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<property name="body"><![CDATA[h4. (as of April, 2015)


h1. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

{*}21.5m (BAD)*  
Now with bad connector...
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos \[here\|^Image 2.jpg\|crystals\] and\[here\|^Image 3.jpg\|inside\].

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)

*15.2m (BAD; bad BSR?)*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]

(shockles 1-4 used in SoCal ECOHAB-2013 and Monterey Bay ECOHAB-2013, but unclear which used when )

h4. ESP-001

* 44 days during Catalina (April 2014) deployment
* Moran MB deployment (Sep/Oct 2014)

h4. ESP-002

\\

h4. ESP-003

* &nbsp;32 days S. Cal ECOHAB w/Mack (Apr 2014)

h4. ESP-004

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).

h4. ESP-005


h1. Anchor lines

\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4.


h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\
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<property name="body"><![CDATA[h4. (as of July, 2014)


h1. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m (bare)*

*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

*21.5m*

Now (Apr 2014) with bad connector...
* Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos [here|^Image 3.jpg|corrosion] and [here|^Image 2.jpg|salt crystals].

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)

*15.2m*
* 41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]

(shockles 1-4 used in SoCal ECOHAB-2013 and Monterey Bay ECOHAB-2013, but unclear which used when )

h4. ESP-001

* 44 days during Catalina (April 2014) deployment
* Moran MB deployment (Sep/Oct 2014)

h4. ESP-002

\\

h4. ESP-003

* &nbsp;32 days S. Cal ECOHAB w/Mack (Apr 2014)

h4. ESP-004

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).

h4. ESP-005


h1. Anchor lines

\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4.


h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\
\\]]></property>
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<property name="body"><![CDATA[h4. (as of April, 2015)


h1. Surface Mooring Cables

*35.5m (w/ floats)*
* 35 days S. Cal ECOHAB w/ Bruce (Mar 2013)
* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

*25.5m*


*25.3m*
* 24 days as Catalina Island replacement (April 2014).&nbsp; Installed April 8, recovered May 1.

{color:#ff0000}{*}21.5m (BAD)*{color}
{color:#ff0000}Now with bad connector...{color}
* {color:#ff0000}Catalina Island (April 2014).&nbsp; Deployed March 18.&nbsp; Failed after 4 days.&nbsp; Used for total of 21 days.&nbsp; Leakage into bottom bell, which corroded power pin.&nbsp; 'Popped' when we opened it.&nbsp; Photos{color} {color:#ff0000}[{color:#ff0000}here{color}|^Image 3.jpg|corrosion]{color} {color:#ff0000}and{color} {color:#ff0000}[{color:#ff0000}here{color}|^Image 2.jpg|salt crystals]{color}{color:#ff0000}.{color}

*15.6m*
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 32 days S. Cal ECOHAB w/Mack (Apr 2014)

{color:#ff0000}{*}15.2m (BAD; bad BSR?)*{color}

* {color:#ff0000}41 day MB ECOHAB w/Bruce (Sep 2013)&nbsp;{color}

h1. Drifter Cables

28.5m (bare)

22.0m (w/ floats; pins #2 and #5 bad)

8.0m (w/ floats)&nbsp;
\\

All cables have lengths etched into the upper cone (the one that attaches to the buoy).

Usage stats will be added as we use them.

h1. Shockle Usages (started keeping track in 2014)


h3. [shockle and line lengths|^shockle-line lengths.xlsx|lengths .xls]

(shockles 1-4 used in SoCal ECOHAB-2013 and Monterey Bay ECOHAB-2013, but unclear which used when )

h4. ESP-001

* 44 days during Catalina (April 2014) deployment
* Moran MB deployment (Sep/Oct 2014)

h4. ESP-002

\\

h4. ESP-003

* &nbsp;32 days S. Cal ECOHAB w/Mack (Apr 2014)

h4. ESP-004

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).

h4. ESP-005


h1. Anchor lines

\\

h4. 11m

* 32 days S. Cal ECOHAB w/Mack (Apr 2014)&nbsp;
* 41 days MB ECOHAB w/Mack (Sep 2013)
* 35 days S. Cal ECOHAB w/Mack (Mar 2013)

h4. 21m

* 35 days S. Cal ECOHAB (Mar 2013)

h4.


h4. 23.4m

* 32 days S. Cal ECOHAB w/Bruce (Apr 2014).&nbsp;

h4. 45m

* 41 days MB ECOHAB&nbsp; (Sep 2013)

h4.


h4. 159m

* 44 days during Catalina (April 2014) deployment

h4.

\\
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<property name="body"><![CDATA[ESP team, please add to the questions:
* What will be the typical length of deployment for the Gen 3 instrument (G3)?
* What is the overall energy budget?
* Do we need our own power source or use the AUV?
* What size will the G3 be designed for?&nbsp; LRAUV size, El Dorado size, or something else?&nbsp;
* Maximum Depth
* Maximum Sampling Depth?

* What is the main function of the G3 instrument?&nbsp; Front end water processing, creating a lysate for back-end analysis?&nbsp; Or will the G3 do more than that? What?
* If simply water processing:
** how much water will be filtered?
** What will be the filtering system?&nbsp; pucks? modified pucks?&nbsp; scintered frits? something else?
** what lysate volume do you want to create?
** Will archival be necessary?

* If G3 runs assays, how many assays/tests will it be running?&nbsp; Frequency?
* Reusable assay's?
* How will decon occur?

LRAUV Payload Specs:
* 300m design depth
* Typical payload size: \~11.5" dia, 12" long
* Maximum payload size \~11.5" dia, 24" long
* Must be neutrally bouyant
* Must include presure housings and buoyancy (if needed)
* AUV power may be used, with reduced range/duration.]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}


{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound. ]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
# [2014 Deployments]
# [2015 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]
# [May 20]
# [May 27]
# June 3
# June 10
# [June 17]
# June 24 \-\- Scott led
# July 1 \-\- Doug led
# [July 8]]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB Timeline |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.3|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1.3%2028_12_2007.doc]
# [PCR Users Manual v1.0|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20PCR%20Module%20Users%20Manual%20V1.0.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram4-07-08.ppt]
# [Redesigned ASV |http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://oceana.shore.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

h3. &nbsp;Results

# [Results Folder |http://oceana.shore.mbari.org/ProjectLibrary/ESP/PCR%20Module%20(LLNL)/PCR%20Results/]]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Kevin, Wayne, Jim, Doug, Brent, Cheri, Chris S., Scott

h3. Machine Builds

* Cores/MFB's:
*# MFB#2 goes on Betty.&nbsp; Thermally calibrated; working on slug positioning
*# MFB#3 goes on Gordon.&nbsp; Monika wrassling with to get it to work....
*# MFB#4 and #5 are from Mclane.&nbsp; Notice very sticky syringes.&nbsp; Cheri trying to whip them into shape.
*# Betty and Gordon are finished with cold-testing.&nbsp;
*# Moe is ready for the new box Jim S. has built. Box should be ready today.&nbsp; Cheri has&nbsp; few connectors to add to box top.

* Gordon and Betty both need new CBV lines.
* Brent mentioned problem Monika having w/ re-setting of valve; Scott will look into it.

h3. MFB


h3. Drifter&nbsp;


h3. Software

* Gordon to get the new GUI branch of software next week.&nbsp; Brent to talk to Monika.&nbsp; Perhaps they'll unhook MFB#3 and run a test protocol just to give Kevin some data.&nbsp; This should happen early/mid next week.

h3. Deep ESP/DWSM

* PISSer
** Doug building.&nbsp; Should be finished early next week.

h3. GUI


h3. Deployment Issues

* Sept 24 is next big surface deployment.&nbsp; Moe w/PCR will go at M0.&nbsp; Mack and Bruce, doing HAB work will be in the north Bay--locations to be determined by John Ryan.&nbsp; Slight move of antenna at Abe's house should hit M0 and north Bay.&nbsp; Will attend to when we know of n. bay location.&nbsp; Priority list is as follows:
**# Moe at M0
**# Betty on MARS
**# Bruce and Mack in N. Bay
**# Gordon on Pier deployment

h3. &nbsp;Other Items]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Wayne, Jim, Doug, Brent, Cheri, Chris S., Scott


h3. Machine Builds

* Cores/MFB's:
*# MFB#2 goes on Betty.&nbsp; Thermally calibrated; working on slug positioning
*# MFB#3 goes on Gordon.&nbsp; Monika wrassling with to get it to work....
*# MFB#4 and #5 are from Mclane.&nbsp; Notice very sticky syringes.&nbsp; Cheri trying to whip them into shape.
*# Betty and Gordon are finished with cold-testing.&nbsp;
*# Moe is ready for the new box Jim S. has built. Box should be ready today.&nbsp; Cheri has&nbsp; few connectors to add to box top.

* Gordon and Betty both need new CBV lines.
* Brent mentioned problem Monika having w/ re-setting of valve; Scott will look into it.

h3. MFB


h3. Drifter&nbsp;


h3. Software

* Gordon to get the new GUI branch of software next week.&nbsp; Brent to talk to Monika.&nbsp; Perhaps they'll unhook MFB#3 and run a test protocol just to give Kevin some data.&nbsp; This should happen early/mid next week.

h3. Deep ESP/DWSM

* PISSer
** Doug building.&nbsp; Should be finished early next week.

h3. GUI


h3. Deployment Issues

* Sept 24 is next big surface deployment.&nbsp; Moe w/PCR will go at M0.&nbsp; Mack and Bruce, doing HAB work will be in the north Bay--locations to be determined by John Ryan.&nbsp; Slight move of antenna at Abe's house should hit M0 and north Bay.&nbsp; Will attend to when we know of n. bay location.&nbsp; Priority list is as follows:
**# Moe at M0
**# Betty on MARS
**# Bruce and Mack in N. Bay
**# Gordon on Pier deployment

h3. &nbsp;Other Items]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision
# [25Jun2009]
# 02Jul2009 -- no meeting; 4th of July break
# [09Jul2009]
# [16Jul2009]]]></property>
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<property name="body"><![CDATA[h3. In future, before starting to thrash, here are some commands
to help ascertain the state of the ESP:


*Flush.location*
&nbsp;Shows where the flush puck is

*clamp.contains&nbsp; #PC* or *CC*
&nbsp;What puck the Clamp contains (if any)

*Storage.pucks.sort*
&nbsp;shows a sorted list of the number of pucks in each tube

*Storage.pucks\[tube#\]=nil*
&nbsp;Causes the software to forget how many pucks were in tube#

*Storage.pucks\[tube#\]=n*&nbsp; #where n is a number
&nbsp;Sets the number of pucks in tube# to n

*Storage.pucks\[tube#\]+=j*
&nbsp;Adds j pucks to the software's record of the number of pucks in tube#

*Storage.pucks.clear*
&nbsp;Causes the software to forget how many pucks were in all tubes

*Flush.to clamp&nbsp; #PC* or *CC*
&nbsp;A safer alternative to clamp.loadFlush

*Flush.garage*
&nbsp;A safer alternative to clamp.unloadFlush

*Arm*
&nbsp;Shows where the arm is

*Arm.owner*
&nbsp;Shows which thread owns the arm

*Flush.owner*
&nbsp; Shows which owns the flushpuck

*Arm.changeOwner Thread.current, :force*
*Flush.changeOwner Thread.current, :force*
&nbsp;Changes the owner of the Arm or FlushPuck to the current thread]]></property>
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<property name="body"><![CDATA[h3. In future, before starting to thrash, here are some commands
h3. to help ascertain the state of the ESP:

*Flush.location*
&nbsp;Shows where the flush puck is

*clamp.contains&nbsp; #PC* or *CC*
&nbsp;What puck the Clamp contains (if any)

*Storage.pucks.sort*
&nbsp;shows a sorted list of the number of pucks in each tube

*Storage.pucks\[tube#\]=nil*
&nbsp;Causes the software to forget how many pucks were in tube#

*Storage.pucks\[tube#\]=n*&nbsp; #where n is a number
&nbsp;Sets the number of pucks in tube# to n

*Storage.pucks\[tube#\]+=j*
&nbsp;Adds j pucks to the software's record of the number of pucks in tube#

*Storage.pucks.clear*
&nbsp;Causes the software to forget how many pucks were in all tubes

*Flush.to clamp&nbsp; #PC* or *CC*
&nbsp;A safer alternative to clamp.loadFlush

*Flush.garage*
&nbsp;A safer alternative to clamp.unloadFlush

*Arm*
&nbsp;Shows where the arm is

*Arm.owner*
&nbsp;Shows which thread owns the arm

*Flush.owner*
&nbsp; Shows which owns the flushpuck

*Arm.changeOwner Thread.current, :force*
*Flush.changeOwner Thread.current, :force*
&nbsp;Changes the owner of the Arm or FlushPuck to the current thread]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 18 Feb 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [MFB-PCR distribution list] as of 03Mar2010]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables]
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h2.


h1. We currently (12-2012) have three Melo trackers

{color:#006600}The Melo is the 'watch-circle' warning transponder for surface moorings.{color}\\

IMEI numbers:

h3. *300034012090780&nbsp; (purchased June, 2011)*


h3. 300234060016190&nbsp; (serial # 122)&nbsp;&nbsp; (both purchased Dec, 2012)


h3. 300234060014550 (serial # 123)


h2.

(IEMI number for Sable 5000 on D-ESP:&nbsp; 300034012099780)

h1.

User's Manuals
# [Quick Start Guide v1.2|^Xeos_Melo_manual-1.pdf|quick start]
# [User Manual v1.5|^Melo_User_Manual _watch_circle_V1.5.pdf|Full Manual]
# [Watch Circle Console User Manual v2.1|^Xeos_Melo_manual-3.pdf|watch circle]\\
# [Xeos pricing changes as of Jan 2013|^Xeos_Iridium_BillingProcess_CustomerLetter.pdf]]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# CVS client
# gcc
# yacc

h3. Steps to build and run

# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:
{code}
cvs checkout ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  Now there are patches that MBARI needed to use over the ruby 1.6.8 that is used to run the ESP instruments.  In order to build ruby 1.6.8 for your machine that you can use to run the ESP stack, first copy the ruby source files from the tar.gz file into the directory where the mbari patches are located.
{code}
$ cd ESP/gen2/software/ruby/ruby-1.6.8-mbari
$ tar --keep-old-file --strip-components 1 -xzf ../snapshot-1.6.tar.gz
{code}
This will populate the patch directory with the ruby source files without overwriting the patches.
# Now run configure.
{code}
./configure
{code}
# Now run make.
{code}
make
{code}
# If all goes well, ruby will have built and you can install by running this as 'root'.
{code}
make install
{code}
# After that, ruby should be ready to go and if you type
{code}
ruby --version
{code}
You should see something like:
{code}
ruby 1.6.8-mbari7/0x4770 (2009-1-19) [i686-linux]
{code}
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run 
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

h4. {color:#ff00cc}Puget Sound{color}

_{+}Lummi Bay:+_

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)

*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.&nbsp; Subsequent investigation found that modem card had been cancelled with T-Mobile due to NOAA miscommunication.&nbsp; When new one was tried, operator did not know to 'close the door' on the modem in order to power the card.&nbsp; Brent flew up and fixed.&nbsp; Missed 4 days of sampling.


*August 18*\--Lummi Bay deployment ended.&nbsp; Machine returned to NOAA.


_{+}Samish Bay:&nbsp;+_

*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; No CTD.&nbsp; Both machines have MFB and PCR.&nbsp; Media event was July 18.

Aug 14--Recover Gordon

Aug 17--Deploy (swap) NEO. \\

h4. {color:#ff00cc}ECOHAB/CANON--Monterey Bay{color}


*&nbsp;September 10, 2013*\-\- Deploy 2 ESP's in Monterey Bay.&nbsp; First time in southern part of bay.

'North'
ESP-Mack\\

'South'
ESP-Bruce
\\]]></property>
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<property name="body"><![CDATA[This page documents some of the HMI/SCADA packages that are available for Java that we might use to build the instrument state GUI.  Here is a table documenting the aspects of the various frameworks:

||Framework||Company||Description||URL||Cost||Licensing||Notes||
|MIStudio|ErgoTech|An intuitive drag-and-drop tool that lets you easily build secure Manufacturing Intelligence, Factory Automation and SCADA System. Design with one tool, deploy to Windows, Linux, J2EE, OSGi and headless embedded systems. View in any browser, on your PDA, or even on your Phone - any environment that supports a Java Applet.|http://www.ergotech.com/index.html|$2500|Web based (applets) so doesn't seem to be a licensing cost for deployment|Since it is applet, probably not going to work for us.  Looks heavily focused on packaged HMI, not really a general framework so that is not great.  Also did not see much in the way of support on their web site (no manuals, wikis, etc.)|
|GLG Toolkit|Generic Logic|GLG's extensive library of dials and meters, gauges, graphs, process control widgets and other graphical components is built on top of the Toolkit's object engine - an approach radically different from the traditional methods of creating programming components.|http://www.genlogic.com/components.html| | |This looks like a pretty nice option.  The have a widget catalog here: http://www.genlogic.com/widgets.html and probably would cover what we would use it for.|
|JSENT|JSENT|JSENT is a pure Java-based Supervisory, Control and Data Acquisition SCADA software product that runs on both Windows and Linux.|http://www.jsent.co.za/index.html|?| |This looks like an actual application so it really doesn't fit our needs|
|Factory PMI|Inductive Automation|A web-launched, database driven plant management interface suite. Featuring SQLTags. |http://www.inductiveautomation.com/products/factorypmi/|$3500|$0|This is a turn-key solution and really doesn't fit what we need.  Licensing would be OK and the delivery looks like JWS, but not sure how customizable it will be and probably cannot be integrated into our appliation.|
|JPC|Net Module|Easy to use (drag and drop) HMI development tool. Engineers without Java programming experience can build their HMIs. The product bundle 'JPC Framework' comprises the JPC Components 'JPC Client', 'JPC Server' and 'JPC Ambassador'. It is the basic product and you must acquire it when you start developing your JPC application. All other JPC Components are separate products.|http://www.netmodule.com/en/products/netmodule_jpc/|?|?|Looks like a large package really tailored to connect up with factory floor systems and provides a tool for drag-n-drop GUI building for HMI.  Probably more than we want and not sure we could break out the component from the GUI builder.|
]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP-Mack w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.5m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP-Bruce w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 5.6m
Location: \-121.9364 36.9047

h4. {color:#ff00cc}Next{color}

*Set xx*]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB \-\- Monterey Bay{color}

Two instruments, one north, one south.

*May 11, 2015*

Deployed ESP-Mack w/ CTD in southern location.&nbsp; Running HAB/DA only.
Can depth \~4.2m but wide tidal swings.
Location: \-121.8789 36.6393

Transit north but weather turned very windy and could not deploy ESP-Bruce.

*May 12, 2015*

&nbsp;Left Santa Cruz and Deployed ESP-Bruce w/ CTD in northern location.&nbsp; Running HAB/DA.
Can depth ~ 6.0m
Location: \-121.9364 36.9047

h4. {color:#ff00cc}Next{color}

*Set xx*]]></property>
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<property name="body"><![CDATA[This page documents some of the HMI/SCADA packages that are available for Java that we might use to build the instrument state GUI.  Here is a table documenting the aspects of the various frameworks:

||Framework||Company||Description||URL||Cost||Licensing||Notes||
|MIStudio|ErgoTech|An intuitive drag-and-drop tool that lets you easily build secure Manufacturing Intelligence, Factory Automation and SCADA System. Design with one tool, deploy to Windows, Linux, J2EE, OSGi and headless embedded systems. View in any browser, on your PDA, or even on your Phone - any environment that supports a Java Applet.|http://www.ergotech.com/index.html|$2500|Web based (applets) so doesn't seem to be a licensing cost for deployment|Since it is applet, probably not going to work for us.  Looks heavily focused on packaged HMI, not really a general framework so that is not great.  Also did not see much in the way of support on their web site (no manuals, wikis, etc.)|
|GLG Toolkit|Generic Logic|GLG's extensive library of dials and meters, gauges, graphs, process control widgets and other graphical components is built on top of the Toolkit's object engine - an approach radically different from the traditional methods of creating programming components.|http://www.genlogic.com/components.html| | |This looks like a pretty nice option.  The have a widget catalog here: http://www.genlogic.com/widgets.html and probably would cover what we would use it for.|]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}Place{color}

Details.

*Date*

What'd we do.

*Sept 25*]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables]
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# Cartridge testing
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables]
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
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# [Cartridge assembly document from Accel [|https://oceana.mbari.org/confluence/users/insertlink-draft-uploadfile.action#|Accel assembly document]]]></property>
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<property name="body"><![CDATA[Software Revision level for Instrument Moe
OS
Ruby
Protocol
Firmware]]></property>
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# \[Cartridge assembly document from Accel\|^Cartridge assembly procedure.docx\| cartridge build procedure\]]]></property>
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<property name="body"><![CDATA[Software Revision level for Instrument NEO
OS
Ruby
Protocol
Firmware]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision
# [25Jun2009]
# 02Jul2009 -- no meeting; 4th of July break
# [09Jul2009]
# [16Jul2009]
# [23Jul2009]]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]
# [Feb 16]
# Feb 23 \-\- Oceans Mtg., Portland
# [Mar 2]
# [Mar 9]]]></property>
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<property name="body"><![CDATA[h3. Discussion Topics:

+\-Upcoming May 27-28 deployment+

Decision: &nbsp;Will set out 2 instruments. &nbsp;Mack, and a turned-around Bruce.
Plan: &nbsp;

&nbsp;&nbsp;&nbsp; Tuesday AM: &nbsp;Boat team--Scott, Doug, Chris S.
&nbsp;&nbsp;&nbsp; Tuesday PM: Bruce refurbish team\- Roman, Nilo, Chris P, Doug
&nbsp;&nbsp;&nbsp; Weds AM: Boat team--Scott, Jim, Doug

+\-Personnel Vacations+
&nbsp;&nbsp;&nbsp; Preliminary vacation plans discussed

+\-Board Bullets+

&nbsp;&nbsp;&nbsp; Team asked for pertinent self-promoting items to present to Board.

h3. Tech Transfer

•&nbsp;&nbsp; &nbsp;Lube on ball-screws--grease chosen and all will be lubed from now on
•&nbsp;&nbsp; &nbsp;Radio-modem box leakage--Scott to work on leaking Bruce radio box once mooring is in on Tuesday
•&nbsp;&nbsp; &nbsp;Status of 2nd mooring--not finished, but Scott working on today
•&nbsp;&nbsp; &nbsp;NEO heaters not starting unless power-cycled--issue to keep an eye on.&nbsp; Unclear what is causing it; possible static discharge on dwarf
•&nbsp;&nbsp; &nbsp;Mack hand slippage update--it's been tightened and run in the cold.&nbsp; No slippage.&nbsp; Not an ideal fix, but we don't know what went wrong initially
•&nbsp;&nbsp; &nbsp;Al vs. SS. on valve coupling-\-{color:#3300ff}Aluminum{color} is the chosen material for valve coupling

h3.


h3. MFB

•&nbsp;&nbsp;&nbsp; First successful amplification occurred yesterday with a slug pulled into top of PCR module line.&nbsp; Addie cleaned ATV and input line #13, drew premixed slug into PCR through these; failed.&nbsp; Deconned and repeated yesterday's experiment.&nbsp; Results not [good|^TAM Tests 5_11_08.xls].&nbsp;
•&nbsp;&nbsp;&nbsp; Encoders.&nbsp; Box of extra encoders cannot be found.&nbsp; Cheri put in order for PO # 0810834 to Measurement Specialties for 100 encoders \-\- placed on 4/24/08

h3. Software

•&nbsp;&nbsp; &nbsp;How to avoid vapor lock on first sample after canning the ESP?--Solution decided was to fill line with fluid, then pull vacuum using a syringe to draw bubble back out intake line.&nbsp; Will try tuesday when canning Mack.
•&nbsp;&nbsp; &nbsp;procedures for uploading images from the buoy--Brent implored the use of the 'upload' command rather than pull images directly off the buoy.&nbsp; Otherwise, one must wait for the hourly update of images on ESPSHORE.
•&nbsp;&nbsp; &nbsp;Logging and displaying processed ISUS data

h3. DWSM

•&nbsp;&nbsp; &nbsp;schedule CDR

h3. GUI development


h3. Other Items

•&nbsp;&nbsp; &nbsp;Planning for 2009 proposal (Attached is Chris's First Pass)

May 22&nbsp;&nbsp; &nbsp;Discuss the plan for the next 4 weeks RE: 2009 proposal
May 30&nbsp;&nbsp; &nbsp;Note this meeting is MOVED one day, to FRIDAY, due to the Ocean Sciences Meeting.&nbsp; Have 'nailed' our projections for 2008.
June 5&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Have 'nailed' our 2009 projections
June 12&nbsp;&nbsp; &nbsp;Have abstract ready (due July 1).&nbsp; Chris will be gone June 14-July 9(?) .&nbsp; I'll be gone June 13-June 29.]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]]]></property>
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<property name="body"><![CDATA[h1. Engineering mtg

Present: Birch, Jensen, Roman, Pargett,  Preston, Marin


Absent: Scholin, Everlove


h1. S. California

\\

1.&nbsp; Pre-trip:&nbsp; Will be week of March 15.&nbsp;
* Probably Tuesday, March 16.&nbsp; Birch/Jensen/Roman
* Will fly into John Wayne Airport, but waiting to hear answers to  many questions from Burt/Matthew.
* Will take Shana Rae.&nbsp; Load mooring gear on Thursday, March 25 in  Moss Landing, then drive ESP's down in van on 30th.&nbsp; Load on ship on  31st.&nbsp; Deploy April 1.
* Divers. Looking into using local divers.&nbsp; Doug Conlin has contact  with local UCLA group.&nbsp; Brent also has some leads.
* Moorings:&nbsp; Jims Scholfield should have them finished by March 17.&nbsp;  Training Paul C. while he makes these two.
* Foam blocks arrive March 29.&nbsp; We will scavenge from exisiting E/M  while these blocks are out being machined.&nbsp; Will end with 3 'short' and 2  'longer' E/M cables.
* Batteries arrive March 10 and be assembled by March 17.
* Will need new anchor lines but need to verify depth

h1. Other issues

A.&nbsp; Betty and hand problem
* Betty is not deployable.&nbsp; We cannot recreate the problem (presumed  to be a short somewhere) to know where to test/what to replace. Vexing.&nbsp;  Will continue to exercise the hand, hoping that use will cause  failure....

B.&nbsp; Doug--update on DWSM
* Problem was that we weren't reliably able to see empty or squeeze,  so we didn't know when to stop pumping.&nbsp; We could change the code to  look for a current increase in the pump, but that's kind of a hack.&nbsp;  Doug to test for another week, then power down to allow Scott access to  battery box in order to cast a new one.
* Before that, Chris P. will clean Gordon Lines and remove reagents.

C.&nbsp; Cheri--MFB build update
* MFB builds continue.&nbsp; hope is to have all finished before she  leaves for Mclane (March 15).&nbsp; MFB distribution list is here.

D.&nbsp; Next MFB training will be week of May 24.&nbsp; Will distribute MFB's  in June.]]></property>
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<property name="body"><![CDATA[h1. Engineering mtg

Present: Birch, Jensen, Roman, Pargett,  Preston, Marin

Absent: Scholin, Everlove

h1. S. California

\\

1.&nbsp; Trip-planning
* Paul Dimeo of the Aquarium of the Pacific has been put in touch with Kim Reisenbechler RE: divers.&nbsp; Should have this nailed down by early next week.
* Scott contacted by George and Hai of OCSD.&nbsp; Apparently they needed proof of insurance and liability before allowing us on the roof.&nbsp; they've been directed to Pinto so we are good to go when we recover the antenna.&nbsp; They've made a request for one of them to attend the deployment.&nbsp; Would be very good politically to take one out with us.
* Coast Guard has told Mike Kelly we do NOT need a Notice to Mariners; there are already so many moorings out in that area that we are covered under one or more.&nbsp; Just let them know when we recover.
* We will load on Shana Rae, Thursday, March 25 at 10am.&nbsp; Jim will email Jim this info.&nbsp;&nbsp;
* E/M cables; both fabricated, now to start testing.&nbsp; Float material is being machined.&nbsp; Scott figuring out float spacing.
* new anchor line to arrive by March 24.

Deployment:
* Team will be Roman, Scott, Jim.&nbsp; Brent will be available via phone for troubleshooting (he leaves 9pm April 2)
* Still deciding best way to get equipment down to Newport Beach, but will leave Weds, March 31, load boat and deploy Apr 1, return to MBARI Apr 2.
* Will build a full dress of mooring in high bay before disassembling, so we know we have everything when we arrive down south.

h1. Other issues

A.&nbsp; Betty and hand problem
* hand still flaking and trouble-shooting is in stasis while Cheri in Falmouth and we prepare for deployment.

B.&nbsp; Doug--update on DWSM
* There is now power back to the core.
* New switches and ba adssembly in sampling can with serrated clips; hopefully no leaking now.
* Resample side has not been opened, but will open when kevlar gears come in.&nbsp; Then we'll replace switches in bag.
* Bill Ussler has seen DWSM and better understands what we mean when we say we depressurize water.&nbsp; He leaves on cruise tonight to test our wand fixture at the methane mound to see if depressurization causing clogging with precipitating hydrate.
* Need to double-check weights and&nbsp; space on WF.&nbsp; Find out how many hours from port the location is.&nbsp; this will help decide where we should open ball, should we need to.
* Some minor software development needed for wand--Brent/Doug/Scott to talk about before Brent leaves.
* Scott to talk to Pete G. about ISMS issues:&nbsp; batteries he's getting for us, which housing will we be using to mount to elevator.&nbsp; Must still mount computer in the ball.

C.&nbsp; 2G camera issue

* Original Starlight cameras were good
* Then came out with higher speed USB camera (f series) that did'nt work with our slower USB
* Now they have the r-speed, which seems to work at older, low speeds, but somtimes there are artifacts; restarting makes them go away.
* If our long term goal is to reduce power, Wayne has found board designed to work at 200mW (vs. 2.5W).&nbsp; We should use him to build a carrier board that would benefit both 2G and 3G systems.&nbsp; This goal is good, but will probably not be addressed until our deployment season is well under way.

D.&nbsp; Next MFB training will be week of May 24.&nbsp; Will distribute MFB's  in June.]]></property>
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<property name="body"><![CDATA[h1. Engineering mtg

Present: Birch, Jensen, Roman, Pargett,  Preston, Marin

Absent: Scholin, Everlove

h1. S. California

\\

1.&nbsp; Trip-planning
* Paul Dimeo of the Aquarium of the Pacific has been put in touch with Kim Reisenbechler RE: divers.&nbsp; Should have this nailed down by early next week.
* Scott contacted by George and Hai of OCSD.&nbsp; Apparently they needed proof of insurance and liability before allowing us on the roof.&nbsp; they've been directed to Pinto so we are good to go when we recover the antenna.&nbsp; They've made a request for one of them to attend the deployment.&nbsp; Would be very good politically to take one out with us.
* Coast Guard has told Mike Kelly we do NOT need a Notice to Mariners; there are already so many moorings out in that area that we are covered under one or more.&nbsp; Just let them know when we recover.
* We will load on Shana Rae, Thursday, March 25 at 10am.&nbsp; Jim will email Jim this info.&nbsp;&nbsp;
* E/M cables; both fabricated, now to start testing.&nbsp; Float material is being machined.&nbsp; Scott figuring out float spacing.
* new anchor line to arrive by March 24.

Deployment:
* Team will be Roman, Scott, Jim.&nbsp; Brent will be available via phone for troubleshooting (he leaves 9pm April 2)
* Still deciding best way to get equipment down to Newport Beach, but will leave Weds, March 31, load boat and deploy Apr 1, return to MBARI Apr 2.
* Will build a full dress of mooring in high bay before disassembling, so we know we have everything when we arrive down south.

h1. Other issues

A.&nbsp; Betty and hand problem
* hand still flaking and trouble-shooting is in stasis while Cheri in Falmouth and we prepare for deployment.

B.&nbsp; Doug--update on DWSM
* There is now power back to the core.
* New switches and ba adssembly in sampling can with serrated clips; hopefully no leaking now.
* Resample side has not been opened, but will open when kevlar gears come in.&nbsp; Then we'll replace switches in bag.
* Bill Ussler has seen DWSM and better understands what we mean when we say we depressurize water.&nbsp; He leaves on cruise tonight to test our wand fixture at the methane mound to see if depressurization causing clogging with precipitating hydrate.
* Need to double-check weights and&nbsp; space on WF.&nbsp; Find out how many hours from port the location is.&nbsp; this will help decide where we should open ball, should we need to.
* Some minor software development needed for wand--Brent/Doug/Scott to talk about before Brent leaves.
* Scott to talk to Pete G. about ISMS issues:&nbsp; batteries he's getting for us, which housing will we be using to mount to elevator.&nbsp; Must still mount computer in the ball.

C.&nbsp; 2G camera issue
* Original Starlight cameras were good
* Then came out with higher speed USB camera (f series) that did'nt work with our slower USB
* Now they have the r-speed, which seems to work at older, low speeds, but somtimes there are artifacts; restarting makes them go away.
* If our long term goal is to reduce power, Wayne has found board designed to work at 200mW (vs. 2.5W).&nbsp; We should use him to build a carrier board that would benefit both 2G and 3G systems.&nbsp; This goal is good, but will probably not be addressed until our deployment season is well under way.

D.&nbsp; Spending out of Moore Foundation $$
* Doug to get price for portable He leak detector
* Brent to get models/price for 4 HP computers, and old email about a cheap, low power radio to test
* Scott to get prices on 4 batteries and chargers for running cores in the lab.
* any remaining money will buy reagents through Roman and Chris P. ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Chris S., Brent, Bill, Scott, Doug, Jim, Chris P.

h1. Items


h4. Drifter

* ESP-Moe is machine for Hawaii.
* We will move our Pt. Lobos day from November (originally slated for MARS deployment) to August 10 or 11 for a drifter test-cruise.
* During that test cruise, we will use ESP-Mack, as brains and surrogate core.&nbsp; Moe will be 'on launch pad' and we don't want to jeopardize reagents with a canning procedure.&nbsp;
* We are moving closer on purchase of refrigerated van.&nbsp; Grech has a few final questions to vendor, making sure the van proposed can go on container ships.
* Final Drifter meeting before Brent leaves is TUESDAY, 10:30am after science mtg.
* h6. Drifter Science
* Must contact Julie to let her know MOE is ready (after checking with Roman)
* Will set up weekly science meetings to track preparation progress toward Hawaii

h4. WHOI

* Bruce still not recovered; we could not get boat for this weekend.&nbsp; Looks like June 10 is soonest to try.
* Chris saw the buoy bottom cone and said it looks like wrench marks on the cone and that the cable had been cut.&nbsp; Unclear, but we should think about overtly linking buoys with MBA (as people equate MBA and MBARI), given their Seafood watch program may be seen with suspicion by the fishing industry in the northeast. We need better Public Relations in the future, just in case, letting fishermen know what the instrument is doing.

h4. JdF Preparations

* Wand 'code' is very simple; on or off of two separate pumps.
* temperature probe on wand tip needs calibration validation.&nbsp; Bill to work with Brent on this this PM.
* ISMS and fixed temp probe to arrive from Harvard today or tomorrow.&nbsp; Will integrate next week.
* ISUS.&nbsp; Doug ordered him more 6-40 screws, but haven't heard from Luke.&nbsp;&nbsp;
* Now that we will have Iridium tracker decision is to use Acoustic Recall to return D-ESP to surface.
* Chris P. has workable mission script.
** Testing still needed:
**# Test temp probe calibration and validate.
**# Test low voltage code (turn stuff off before we run out of juice)
**# Test sampling at cold temperature
**# move code to flash memory
**# run (3?) full phases
**# communications path

* Decision is to close sphere on Thursday, June 9 before Scott leaves on the 10th for vacation.]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] \- first discussion of adaptive sampling strategies
# Mar 3 - CMORE Hawaii
# [Mar 10] \-\- wand schematic
# [Mar 17]
# [Mar 24]
# Mar 31 - team deploying MOE at M0; Brent at WHOI
# [Apr 7]
# [Apr 14]
# [Apr 21]\--wand schematic reminder...
# [Apr 28]\--D-ESP 2-Year Birthday Celebration\!\!&nbsp; (Poster is [here|^ESP Birthday Poster(smaller).pdf])
# May 5 \-\- Visit to ASU
# [May 12]
# [May 19]
# [May 26]]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]
# [Feb 16]
# Feb 23 \-\- Oceans Mtg., Portland
# [Mar 2]
# [Mar 9]
# Mar 16 \-\- Jim in S. Cal scouting.  John Ryan ran mtg.
# Mar 23
# Mar 30
# Apr 6 \-\- canceled in preparation for M0 deployment
# Apr 13
# Apr 20
# Apr 27 \--AbSciCon, League City TX
# [May 4]
# [May 11]
# [May 18]]]></property>
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<property name="body"><![CDATA[Present:&nbsp;&nbsp; Brent, Jim, Scott, Doug, Chris P, Roman, John R., Julie


Absent: Chris S.

h3. Announcements:

1.&nbsp; OTIC kick-off meetings will be Nov 11 and Jan 13.&nbsp; Clem Furlong and the UW crew will be here both days.&nbsp; Laurie Connell and Greg Doucette will come in Jan.&nbsp; Annette handling travel/lodging arrangements.

2.&nbsp; Quick review of where to charge hours.&nbsp; Most work is now going on .00 sub-projects, except for occasional things Doug P is doing.&nbsp; Email went out detailing who charge what.&nbsp; If you weren't notified and you need to charge SURF Center, time goes on 900915 or 900913.&nbsp; Check with Jim.

h3. Issues:

* John R brought the LISST for show-and-tell, and discuss mounting options on one of the surface moorings (bight or shadow) during BIOSPACE.&nbsp; Looks like it will fit in the ISUS position with relatively little modifcation.&nbsp; Doug to get diameter before John sends back for calibration, John to get in-water weight and collect battery housing.

* Strain Relief.&nbsp; The strain relief on the can end of drifter appears to have failed.&nbsp; It again appears to be a manufacturing flaw.&nbsp; Scott thinks it will make it through tomorrow's deployment, but should be replaced before CANON cruise.&nbsp; Jim will check with Dale/Scholfield whether there is time to reterminate before CANON.&nbsp; We will use the recently rec'd new strain relief and again send this one back.

* Brent rec'd the 8MB board from McLane, and the 16MB they had ordered and shipped here.&nbsp; He quickly ascertained the problem and notified Ivory, who is on vacation until next week.&nbsp; This episode has Brent believing he needs better access to their network; things can be fixed from here, instead of fed-exing back and forth.

* New camera testing.&nbsp; Images look good, but anything coarser than 2x2 binning will show a pixel shift, due possibly to our slow processor.&nbsp; Chris P and Roman said 4x4 binning no longer used, so this is moot point.&nbsp; Brent will do a cold test, but this new camera (Starlight model 'R') is looking good.

* Pressure issues:&nbsp; Thanks to work of chris P., we have settled on pressures that 'work':&nbsp; {color:#ff0000}{*}55psi for SH1, 40psi for WCR{*}{color}. &nbsp; All machines will be changed to these, and Doug is looking at the availability of springs that, instead of being 2x current strength, may be only 1.3-1.4x.&nbsp; Increasing spring strength has consquences of ball screw selection and connection to the motor.&nbsp; All permutations being evaluated.&nbsp; We need to get this info to McLane as soon as we see how stiffer springs function.\\

h5. +Machines+


h6. Bruce

Tina's assays were not working.&nbsp; Roman ran several from 2008; they worked perfectly.&nbsp; thought was something in the filter media could be causing issue.&nbsp; But then Roman ran more of Tina's this morning and it worked.&nbsp; We will continue to run Bruce up until BioSPACE to ascertain the problem.


h6. Mack

Mack is working.&nbsp; Connector on PSV seems no longer flakey, and with the lowered puck pressures and recalibrated pressure sensors, we are ready to can today, mounting on Drifter tomorrow AM.&nbsp; Roman taking out tomorrow for 3rd test.


h6. MOE

Ready for running.&nbsp; MOE should get the very latest software, which was a check to keep heaters from heating to temperatures that could never be reached.


h6. NEO

currently in water at M0. will get latest firmware when recovered (Aug 30)

Must decide what Science wants to do with NEO.&nbsp; Will there be a pier  deployment in Oct/Nov, and do we rid NEO of the tombstone and replace  with an MFB and the attendant firmware upgrades, so all cores will be  running the same thing?&nbsp; Discuss this at next Tuesday's science mtg.

h6. Gordon

Still in the ball.


h6. Betty

may become testbed for clamp spring testing.


h3. Communications for BIOSPACE

Scott heading to Abe's house next Tuesday (Aug 24) give him his 2010/2011 check, and oversee the antenna post install for this new antenna.&nbsp; He'll call Abe and antenna guy on Monday to confirm.]]></property>
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<property name="body"><![CDATA[In order for McLane to get access to the source code for the ESP, it was deemed that a CVS server in the DMZ with the source code rsync'd out was probably the best option. The machine prey.mbari.org was deemed as the best fit.  In order to configure prey for this work, the following steps were taken:

# Logged in a root
# ran up2date cvs to install the cvs and received the following:
{noformat}
[root@prey home]# up2date cvs

Fetching Obsoletes list for channel: rhel-ia64-es-4...

Fetching rpm headers...
########################################

Name                                    Version              Rel               Arch
----------------------------------------------------------------------------------------
cvs                                     1.11.17             11.el4              ia64  


Testing package set / solving RPM inter-dependencies...
########################################
cvs-1.11.17-11.el4.ia64.rpm ########################## Done.                   
Preparing              ########################################### [100%]

Installing...
   1:cvs                    ########################################### [100%]
[root@prey home]# 
{noformat}
# Created the home directory for cvs
{noformat}
[root@prey home]# mkdir /home/cvs
{noformat}
# I initialized the cvs home directory using
{noformat}
[root@prey cvs]# cvs -d /home/cvs init
{noformat}
This created the CVSROOT directory and populated it with the necessary files.
# I then created the two cvs related groups using
{noformat}
[root@prey cvs]# groupadd cvsusers
[root@prey cvs]# groupadd cvsadmin
{noformat}
# Created a cvs user (and group) using:
{noformat}
[root@prey cvs]# groupadd cvs
[root@prey cvs]# useradd cvs -g cvs
{noformat}
# Added the CVSROOT environment variable by adding the following to /etc/profile
{noformat}
# Export the CVSROOT directory
CVSROOT=/home/cvs

export CVSROOT
{noformat}
# I set the cvs executable permissions so that it can be run as a service
{noformat}
[root@prey bin]# chmod 2755 /usr/bin/cvs
{noformat}
# Finally, I created the file /etc/xinetd.d/cvs and put the following in that file:
{noformat}
 service cvspserver
 {
         disable            = no
         socket_type    = stream
         wait                = no
         user                = cvs
         group              = cvs
         log_type          = FILE /var/log/cvspserver
         protocol          = tcp
         env                 = '$HOME=/home/cvs'
         bind                = 134.89.2.27
         log_on_failure  += USERID
         port                = 2401
         server             = /usr/bin/cvs
         server_args     = -f --allow-root=/home/cvsroot pserver
 }
{noformat}
# I then rebooted prey]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]
# [May 20]
# [May 27]
# June 3
# June 10
# [June 17]
# June 24 \-\- Scott led
# July 1 \-\- Doug led
# [July 8]
# Jul 15 \--Preparation for Methane cruise
# Jul 22 \--Methane cruise
# Jul 29 \--Methane cruise
# [Aug 5]
# [Aug 12]]]></property>
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<property name="body"><![CDATA[Present:

Absent:

1. Updates:
\\
* Moe in      cold room---plan for mid-April deployment?
* Bruce      and DA.&nbsp; Software      Switched?&nbsp; Are we good to go?
* Array      printing update?
* PCR      reagents on Gordon---Chris P. update.
* SPE      columns---still waiting on quote.
\\

2. Progress update on papers:
\\
* Chris      P.
* John      R.
\\]]></property>
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<property name="body"><![CDATA[Present: Jim, Roman, Chris P., Julie, Bill


Absent:&nbsp; Chris S., John


{color:#3300ff}1. Updates:{color}\\
* {color:#3300ff}Moe in      cold room---plan for mid-April deployment?{color}
** Will use NEO for April 14 deployment.&nbsp; Julie to dust it off this week, and next week will discuss where NEO is in preparation for the deployment.
** Probes on Moe:&nbsp; currently using 1 NED (IPC), 2 FAM, rest TAM.&nbsp; So far only 1 positive FAM, and several inhibitions on all channels.&nbsp; Will continue the cold-room test for at least 10 more days.
** Roman giving Julie some deep water collected yesterday.&nbsp; May not have the inhibition that the surface water has.

* {color:#3300ff}Bruce      and DA.&nbsp; Software      Switched?&nbsp; Are we good to go?{color}
** Bruce code was changed to latest (new) code yesterday.&nbsp; Roman firing off&nbsp; a DA today as a final check.

* {color:#3300ff}Array      printing update?{color}
** All tips are working and Roman/Nilo have printed 84 DA arrays.&nbsp; Will QC these this morning; if fine, then Chris P., gets Nilo to start printing the more difficult (longer) BAC arrays.

* {color:#3300ff}PCR      reagents on Gordon---Chris P. update.{color}
** Chris P. to remove reagents this morning.

* SPE      columns---still waiting on quote.
* Chris P. still to check/confirm the IPC order.&nbsp; Sent in the PO, but did not hear that they rec'd it...

{color:#3300ff}2. Progress update on papers:{color}\\
* Chris      P.
** Discussed the Figures; much progress made.&nbsp; Chris will have rough draft of all figures by next week.&nbsp; Much discussion about what should be used to normalize arrays, background or other spots.&nbsp; She will try using several methods.

* John      R.&nbsp;
** Report from John:
** \* BAC:
Working with Chris P. on environmental data to present in her paper

\* HAB:
Nilo and Roman have begun the process of turning array spot intensity into numbers for '08.&nbsp; I stand ready to assist in that processing, if needed, and I am ready to carefully examine how the significant patterns in the HAB time-series relate to the environmental variability (data from moorings, AUV, satellite).&nbsp; The interannual picture was mostly roughed out already, however I furthered the analysis by quantifying wind and hydrographic conditions of the '07 and '08 network deployments as anomalies (deviations from their climatological monthly mean).&nbsp; For example, this showed September '07 to be anomalously weak upwelling, and October '08 to be anomalously strong upwelling.

\* ZOO:
Working with Julio on ESP and AUV results for his paper.]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# Feb 11
# Feb 18 - All-day CANON mtg
# Feb 25 - Oceans Mtg (Portland)
# [Mar 4]
# Mar 11 - Jim at ASU.&nbsp; Scott ran mtg.
# [Mar 18]
# Mar 25 \-\- loading moorings on Shana Rae for trip south
# Apr 1 \-\- deploy in S. Cal
# [Apr 8]
# Apr 15
# Apr 22
# Apr 29
# [May 6]
# [May 13]
# [May 20]
# [May 27]
# June 3
# June 10
# [June 17]
# June 24 \-\- Scott led
# July 1 \-\- Doug led
# [July 8]
# Jul 15 \--Preparation for Methane cruise
# Jul 22 \--Methane cruise
# Jul 29 \--Methane cruise
# [Aug 5]
# [Aug 12]
# [Aug 19]]]></property>
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<property name="body"><![CDATA[No notes.]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [MFB-PCR distribution list] as of 03Mar2010]]></property>
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<property name="body"><![CDATA[we should put a sat tracker on the D-ESP - worth the $ if we can't borrow one. ]]></property>
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<property name="body"><![CDATA[h2. Items


h4. JdF

* &nbsp;With the issues of Harvard's primers, we have decided to install the core into the Ball Tomorrow.&nbsp; No use waiting for their primers to be tested, as nothing seems to work.
* Will set up CTD with the RTD pass-through on *Tuesday* so we can test the wand temperature code before Brent leaves.&nbsp; Scott has seen that voltages get passed through the CTD, but haven't been able to do any more extensive testing.
* ISUS and ISMS are supposed to be ready June 1.&nbsp; Doug has spoken with Luke, and we will use their 2000m rated probe heads.&nbsp; The chamber water must flow through is quite small, which will restrict flow to all instruments downstream, using our new wand flow setup.&nbsp; Thus, will mount ISMS in parallel to ISUS; Doug figures 80% of flow will go through ISMS, rest through ISUS.
* Satellite Beacon on D-ESP.
** Issue:&nbsp; If ship must leave ESP and while we're gone, D-ESP rises to surface.&nbsp; Current radio link is for close proximity only (1-2mi).&nbsp; Several Options:

* *# Make recall of D-ESP only with ROV pull release, no acoustic drop-wt recall.&nbsp; This several lessens chance of unintended lift-off.
*# Could mount ARGOS beacon to elevator.&nbsp; Ken Smith may have one we could borrow.&nbsp; Will ask when they return tomorrow.
*# Could mount Iridium tracker to elevator.&nbsp;

** Both ARGOS and Iridium cost \~$4K, and have a small monthly data-plan charge.

h5. Travel Plans

* &nbsp;Arrivals to Newport:&nbsp; Chris P getting there July 8, engineers getting there July 9 or 10.&nbsp; MOB the 11th.&nbsp; Shove off 12th.
* Departures:&nbsp; We've been told ship will return to port at 4pm, July 23.&nbsp; Probably not enough time to unload and make it back to Portland that day given the afternoon arrival.&nbsp; Teresa says we will be allowed to remain on ship the evening of the 23rd.&nbsp; Thus, de-mob on 24th, and make return plans for that day.&nbsp; Bill staying until 25th to load truck and see equipment off.

h4. WHOI

* The ESP Bruce story being told [here|2011 Deployments].&nbsp;
* WHOI working feverishly to finish ESP-Chris mount and to test their buoy.&nbsp; Should know how/if it works by middle of next week.]]></property>
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<property name="body"><![CDATA[h2. Items


h4. JdF

* &nbsp;With the issues of Harvard's primers, we have decided to install the core into the Ball Tomorrow.&nbsp; No use waiting for their primers to be tested, as nothing seems to work.
* Will set up CTD with the RTD pass-through on *Tuesday* so we can test the wand temperature code before Brent leaves.&nbsp; Scott has seen that voltages get passed through the CTD, but haven't been able to do any more extensive testing.
* ISUS and ISMS are supposed to be ready June 1.&nbsp; Doug has spoken with Luke, and we will use their 2000m rated probe heads.&nbsp; The chamber water must flow through is quite small, which will restrict flow to all instruments downstream, using our new wand flow setup.&nbsp; Thus, will mount ISMS in parallel to ISUS; Doug figures 80% of flow will go through ISMS, rest through ISUS.
* Satellite Beacon on D-ESP.
** Issue:&nbsp; If ship must leave ESP and while we're gone, D-ESP rises to surface.&nbsp; Current radio link is for close proximity only (1-2mi).&nbsp; Several Options:

## Make recall of D-ESP only with ROV pull release, no acoustic drop-wt recall.&nbsp; This several lessens chance of unintended lift-off.&nbsp;
## Could mount ARGOS beacon to elevator.&nbsp; Ken Smith may have one we could borrow.&nbsp; Will ask when they return tomorrow.
## Could mount Iridium tracker to elevator.&nbsp;

* Both ARGOS and Iridium cost \~$4K, and have a small monthly data-plan charge.

h5. Travel Plans

* &nbsp;Arrivals to Newport:&nbsp; Chris P getting there July 8, engineers getting there July 9 or 10.&nbsp; MOB the 11th.&nbsp; Shove off 12th.
* Departures:&nbsp; We've been told ship will return to port at 4pm, July 23.&nbsp; Probably not enough time to unload and make it back to Portland that day given the afternoon arrival.&nbsp; Teresa says we will be allowed to remain on ship the evening of the 23rd.&nbsp; Thus, de-mob on 24th, and make return plans for that day.&nbsp; Bill staying until 25th to load truck and see equipment off.

h4. WHOI

* The ESP Bruce story being told [here|2011 Deployments].&nbsp;
* WHOI working feverishly to finish ESP-Chris mount and to test their buoy.&nbsp; Should know how/if it works by middle of next week.]]></property>
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<property name="body"><![CDATA[h2. Items


h4. JdF

* &nbsp;With the issues of Harvard's primers, we have decided to install the core into the Ball Tomorrow.&nbsp; No use waiting for their primers to be tested, as nothing seems to work.
* Will set up CTD with the RTD pass-through on *Tuesday* so we can test the wand temperature code before Brent leaves.&nbsp; Scott has seen that voltages get passed through the CTD, but haven't been able to do any more extensive testing.
* ISUS and ISMS are supposed to be ready June 1.&nbsp; Doug has spoken with Luke, and we will use their 2000m rated probe heads.&nbsp; The chamber water must flow through is quite small, which will restrict flow to all instruments downstream, using our new wand flow setup.&nbsp; Thus, will mount ISMS in parallel to ISUS; Doug figures 80% of flow will go through ISMS, rest through ISUS.
* Satellite Beacon on D-ESP.
** Issue:&nbsp; If ship must leave ESP and while we're gone, D-ESP rises to surface.&nbsp; Current radio link is for close proximity only (1-2mi).&nbsp; Several Options:

*# Make recall of D-ESP only with ROV pull release, no acoustic drop-wt recall.&nbsp; This several lessens chance of unintended lift-off.
*# Could mount ARGOS beacon to elevator.&nbsp; Ken Smith may have one we could borrow.&nbsp; Will ask when they return tomorrow.
*# Could mount Iridium tracker to elevator.&nbsp;

** Both ARGOS and Iridium cost \~$4K, and have a small monthly data-plan charge.

h5. Travel Plans

* &nbsp;Arrivals to Newport:&nbsp; Chris P getting there July 8, engineers getting there July 9 or 10.&nbsp; MOB the 11th.&nbsp; Shove off 12th.
* Departures:&nbsp; We've been told ship will return to port at 4pm, July 23.&nbsp; Probably not enough time to unload and make it back to Portland that day given the afternoon arrival.&nbsp; Teresa says we will be allowed to remain on ship the evening of the 23rd.&nbsp; Thus, de-mob on 24th, and make return plans for that day.&nbsp; Bill staying until 25th to load truck and see equipment off.

h4. WHOI

* The ESP Bruce story being told [here|2011 Deployments]. \\]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2010 arranged chronologically+ (colors are same deployment)

\\

{color:#ff00ff}April 2, 2010.{color}&nbsp; So. Cal beginning. No PCR.&nbsp; Simply HAB and HAB-DA assays.

Bruce (water = 55m):&nbsp; was dragged about 50m, and ended up about 5m deeper than deployed.
33° 35' 02.1"
118° 2' 05.7"
&nbsp;
Mack (water = 30m)
33° 36' 19.8"
118° 01' 08.7"

{color:#ff00ff}April 29{color} Recover Bruce.&nbsp; Blowing.&nbsp; {color:#ff00ff}April 30{color}, recover Mack.
\\

{color:#339900}April 14 Deploy NEO w/PCR.  Introduced water next day.  several recoveries weathered out.  Finally recovered April 22.{color}
{color:#339900}May 4.&nbsp;{color} Deploy Moe w/PCR to M0.&nbsp; Start of leapfrog series.
{color:#339900}May 25{color}.&nbsp; Recovered Moe and replaced with NEO.&nbsp; This cruise filmed by Melancon.  This was 'hot-swap' cruise.
{color:#339900}June 15{color}.&nbsp; Recovered NEO and replaced with MOE.  This was a 'hot-swap' cruise; can, orange battery boxes, ISUS battery, CTD battery, and GPS batteries all replaced.  mooring and anchor/bungees were re-used.
{color:#ff0000}Pressure problems developed;&nbsp; MOE recovered Jun 23.{color}{color:#ff0000}&nbsp; Discovered pooched o-rings.{color}

{color:#993366}July 22-28{color};&nbsp; Western Flyer Cruise with D-ESP; Gordon and PCR at Methane Mound.

{color:#0000ff}&nbsp;August 3{color};&nbsp; Deploy NEO at M0 with tombstone PCR]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]
# [Feb 16]
# Feb 23 \-\- Oceans Mtg., Portland
# [Mar 2]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h4. {panel:title=Administrative Items|BGcolor=blue|width=100%|borderWidth=4}




h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]
{panel}
{section}
{column:width=50%}
h4. {panel:title=Engineering|borderWidth=2}

{panel}


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{column}
{column:width=50%}
h4. {panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}

{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h4. {panel:title=Administrative Items|BGcolor=blue|width=100%|borderWidth=4}

{panel}


h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]
{section}
{column:width=50%}

h4. {panel:title=Engineering|borderWidth=2}

{panel}


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{column}
{column:width=50%}

h4. {panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
##[JdF Straw Man Schedule\|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
### [MFB-PCR distribution list] as of 4Nov2010
{panel}

{column}
{section}]]></property>
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<property name="body"><![CDATA[Present:

Absent:&nbsp; <!--  /* Font Definitions */ @font-face 	{font-family:"Times New Roman"; 	panose-1:0 2 2 6 3 5 4 5 2 3; 	mso-font-charset:0; 	mso-generic-font-family:auto; 	mso-font-pitch:variable; 	mso-font-signature:50331648 0 0 0 1 0;} @font-face 	{font-family:"Courier New"; 	panose-1:0 2 7 3 9 2 2 5 2 4; 	mso-font-charset:0; 	mso-generic-font-family:auto; 	mso-font-pitch:variable; 	mso-font-signature:50331648 0 0 0 1 0;} @font-face 	{font-family:Wingdings; 	panose-1:0 5 2 1 2 1 8 4 8 7; 	mso-font-charset:2; 	mso-generic-font-family:auto; 	mso-font-pitch:variable; 	mso-font-signature:0 0 256 0 -2147483648 0;}  /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal 	{mso-style-parent:""; 	margin:0in; 	margin-bottom:.0001pt; 	mso-pagination:widow-orphan; 	font-size:12.0pt; 	font-family:"Times New Roman";} table.MsoNormalTable 	{mso-style-parent:""; 	font-size:10.0pt; 	font-family:"Times New Roman";} @page Section1 	{size:8.5in 11.0in; 	margin:1.0in 1.25in 1.0in 1.25in; 	mso-header-margin:.5in; 	mso-footer-margin:.5in; 	mso-paper-source:0;} div.Section1 	{page:Section1;}  /* List Definitions */ @list l0 	{mso-list-id:1771705094; 	mso-list-type:hybrid; 	mso-list-template-ids:-536572960 1907510318 67698691 67698693 67698689 67698691 67698693 67698689 67698691 67698693;} @list l0:level1 	{mso-level-number-format:bullet; 	mso-level-text:?; 	mso-level-tab-stop:.5in; 	mso-level-number-position:left; 	text-indent:-.25in; 	font-family:Symbol;} @list l1 	{mso-list-id:1772554312; 	mso-list-type:hybrid; 	mso-list-template-ids:-609868510 1907510318 67698691 67698693 67698689 67698691 67698693 67698689 67698691 67698693;} @list l1:level1 	{mso-level-number-format:bullet; 	mso-level-text:?; 	mso-level-tab-stop:.5in; 	mso-level-number-position:left; 	text-indent:-.25in; 	font-family:Symbol;} ol 	{margin-bottom:0in;} ul 	{margin-bottom:0in;} -->

1.&nbsp; Updates:\\ * Moe in      cold room---plan for mid-April deployment?
* Bruce      and DA.&nbsp; Software      Switched?&nbsp; Are we good to go?
* Array      printing update?
* PCR      reagents on Gordon---Chris P. update.
* SPE      columns---still waiting on quote.\\ 2.&nbsp; Progress update on papers:
* Chris      P.
* John      R.]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h4. {panel:title=Administrative Items|BGcolor=blue|width=100%|borderWidth=4}




h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]
{panel}
{section}
{column:width=50%}

h4. {panel:title=Engineering|borderWidth=2}




h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}

{column}
{column:width=50%}

h4. {panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
\##[JdF Straw Man Schedule\|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
### [MFB-PCR distribution list] as of 4Nov2010
{panel}

{column}
{section}]]></property>
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<property name="body"><![CDATA[Present:&nbsp;&nbsp; Jim, Scott, Doug, Chris P, Chris S.


Absent: Brent, Roman, Julie


h3. Announcements:

1.&nbsp;


2.&nbsp; Q.

h3. Issues:

* Pressure issues on all cores.
** We believe we've found the problem, which seemed to have become exacerbated when we added the larger o-ring in the PEEK. This gave the puck more surface area to 'push back' on the clamp, and we were operating near the capacity of the springs, thus the pucks would leak/not hold pressure.&nbsp; The fix is relatively simple.&nbsp; Doug has chosen some springs to 'double-up' above and below the puck, and we will go to a softer aluminum coupling b/w motor and ball screw.&nbsp; This pressure issue is only and issue with the fine porosity filters, which are not used in HAB operation, so it is not a critical path issue for McLane, although something they will be notified about.
** Moe will go through it's final check-out next week, and if the current SH1 and WCR pressures work, we will not exchange any springs until after the BIOSPACE deployment.

* E/M cables.
** We currently have 2 'long' and 3 'short' EM cables:
*** LONG
**** one 22m cable is currently on Drifer
**** one 20m cable has an incipient bird-cage near the middle (6m) and needs the bending strain relief (BSR) repaired.
*** SHORT
**** two 15m cables (currently one is deployed w/ NEO, one is here at MBARI)
**** one has end cut off to fix BSR
** We must repair one (to have 5 cables); Scott will decide Monday after talking to Gene/Paul.
** {color:#cc0000}We need to purchase more cable this winter.{color}

* ISUS
** Drawings for ISUS 4K housing are finished and have been checked by Ray (thanks Doug).
** Will have a meeting with Ken Johnson and Luke to approve.
** Also need to discuss what equipment SURF has and wants them to build, so we only need to tap the Johnson group once/year for calibrations.
** Meeting slated for Tuesday, Aug 31, 11am.
** Must also figure out how to power ISUS.&nbsp; Using ESP batteries saves us from $15K battery housing, but does it run off a power converter?

* Spares
** Unknown what spares we have and/or where things are located in the lab.&nbsp; Waiting for Roman to return from vacation and we will do major reorganization, and possible re-order of parts, in particular spare PTV and CTV's.

* Antenna at Abe's house has not been mounted, as it did not arrive on Monday.&nbsp; Scott will work next week to schedule another time.&nbsp; Unlikely to work mounted on fascia.

* MARS wet-mate connector PO (#*1011191)* approved today.

h5. +Machines+


h6. Bruce

Scott and Jim worked on PTV, finding that it does not hold pressure.&nbsp; Found an old used PTV; disassembled, both look similar.&nbsp; We swapped rotors and are pressure testing this combination over the weekend.


h6. Mack

All reagents are on (except HAB/DA).&nbsp; Chris will run WCR/Bac/WCR&nbsp; with runs through the weekend.&nbsp; Monday is puck-fest.&nbsp; Load them on Tuesday, can on Weds and give to Gene on Thurs/Friday.&nbsp; That is also the day of the post-can QC.&nbsp; Drifter gets loaded on Weds, Sep 8.&nbsp; Chris to assemble materials to keep Mack cool.


h6. MOE

Scott fixed broken traces on collection temp sensor.&nbsp; Chris doing series of runs over weekend, getting ready for Julie handoff.


h6. NEO

currently in water at M0. will get latest firmware when recovered (Aug 30).&nbsp; Jim and Scott to get Monday am. 6:30 for 7:00.


h6. Gordon

Still in the ball.

h6. Betty

no report.


h3.]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h4. {panel:title=Administrative Items|BGcolor=blue|width=100%|borderWidth=4}

{panel}


h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]
{section}
{column:width=50%}

h4. {panel:title=Engineering|borderWidth=2}

{panel}


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{column}
{column:width=50%}

h4. {panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
##[JdF Straw Man Schedule|[|https://oceana.mbari.org/confluence/users/insertlink-page-uploadfile.action#|Schedule as of 5-26-2011]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}
# [MFB-PCR distribution list] as of 4Nov2010
{panel}

{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h4. {panel:title=Administrative Items|BGcolor=blue|width=100%|borderWidth=4}

h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]
{panel}

{section}
{column:width=50%}
h4. {panel:title=Engineering|borderWidth=2}




h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}


{column}
{column:width=50%}
h4. {panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
{panel}


h4. {panel:title=Collaboration Items|borderWidth=2}

# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Discussion of 18 Feb 2010

Luke Coletti, Doug Pargett, Jim Birch
# &nbsp;For July, 2010 WF cruise, ESP team will use Johnson lab 1Km housing.&nbsp; There were some issues with the last time it was used; weird readings--discussion ensued as to why readings not normal.
# Doug to draw up plans for pressure housing based on original aluminum design, keeping original diameter, using 2 radial o-rings to seal end caps.
# Doug will draw up plans for probe head opening using the actual probe he has, and getting rid of the current goofy SAE opening.
# We will make 2 Ti housings; ESP pays for 1, Johnson lab pays for 1.
# Eventually we will power the deep ISUS from our Deep-Sea Power and light battery stack, which will allow recharging if needed.&nbsp; But for July we'll use Luke's battery pack (especially since it's such a short deployment).
\\

h1. ISUS specs

&nbsp;Based on Luke's LOBO experiences, one 'single stick' battery pack will power ISUS for 6 months if sampling once/hr.&nbsp; Thus, 20 min sampling rate would last \~1.2 months.&nbsp; Duration scales proportionally.
\\
\\
\\

h1.


h1. Continued Discussion 31 August 2010

Luke, Doug, Scott, Jim, Ken
\\

1.&nbsp; How will we power ISUS on DESP?&nbsp; ISUS runs on 8-20V, 6-7 watts nominal.&nbsp; Current plan is to run off the DESP batteries.

2.&nbsp; Ken said they can build 2 ISUS starting right now.&nbsp; One will be shallow, one deep.&nbsp; We have also asked for 3 deep probes ($2200/ea).

3.&nbsp; Luke will give Doug plans to modify the calibrator, and new flow-cell for calibrations; these are nec with the new titanium housing design.

4.&nbsp; Doug will send [plans|4K housing plans] for Ti housing out for bid.&nbsp; Next steps will be determined by cost/time estimates.&nbsp; Ken has offered us his aluminum housings for deep work.]]></property>
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<property name="body"><![CDATA[h1. Discussion of 18 Feb 2010

Luke Coletti, Doug Pargett, Jim Birch
# &nbsp;For July, 2010 WF cruise, ESP team will use Johnson lab 1Km housing.&nbsp; There were some issues with the last time it was used; weird readings--discussion ensued as to why readings not normal.
# Doug to draw up plans for pressure housing based on original aluminum design, keeping original diameter, using 2 radial o-rings to seal end caps.
# Doug will draw up plans for probe head opening using the actual probe he has, and getting rid of the current goofy SAE opening.
# We will make 2 Ti housings; ESP pays for 1, Johnson lab pays for 1.
# Eventually we will power the deep ISUS from our Deep-Sea Power and light battery stack, which will allow recharging if needed.&nbsp; But for July we'll use Luke's battery pack (especially since it's such a short deployment).
\\

h1. ISUS specs

&nbsp;Based on Luke's LOBO experiences, one 'single stick' battery pack will power ISUS for 6 months if sampling once/hr.&nbsp; Thus, 20 min sampling rate would last \~1.2 months.&nbsp; Duration scales proportionally.
\\ \\ \\

h1.


h1. Continued Discussion 31 August 2010

Luke, Doug, Scott, Jim, Ken \\

1.&nbsp; How will we power ISUS on DESP?&nbsp; ISUS runs on 8-20V, 6-7 watts nominal.&nbsp; Current plan is to run off the DESP batteries.

2.&nbsp; Ken said they can build 2 ISUS starting right now.&nbsp; One will be shallow, one deep.&nbsp; We have also asked for 3 deep probes ($2200/ea).

3.&nbsp; Luke will give Doug plans to modify the calibrator, and new flow-cell for calibrations; these are nec with the new titanium housing design.

4.&nbsp; Doug will send plans for Ti housing out for bid.&nbsp; Next steps will be determined by cost/time estimates.&nbsp; Ken has offered us his aluminum housings for deep work.]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.

{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage taken by Rob Vincent:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]

Map of locations:&nbsp; http://maps.google.com/maps/ms?ie=UTF&msa=0&msid=213220825771739778963.0004a40bdd601babc291d

May 23.&nbsp; Attempted recovery of ESP.&nbsp; Message from Roman:

&nbsp;&nbsp;&nbsp; We went out to the site where espbruce was moored and attempted to find it.&nbsp; The weather was very poor and water was very turbid.&nbsp; Using the ships depth finder we found a promising target.&nbsp; In difficult conditions the divers performed a search but espbruce was not found.
&nbsp;&nbsp;&nbsp; We recovered the mooring.&nbsp; It looks like the cable was pulled straight out of the cone.&nbsp; The top mast is bent but I cannot say if this was caused by a rough landing on the beach or boat impact.&nbsp; There are no dents or gouges on the mooring.&nbsp; The radio box is dry and antenna looks ok.
&nbsp;&nbsp;&nbsp; Thursday the RV Gulf Challenger may be able to survey the area with a side scanning sonar.&nbsp; This will be a much better way to search for espbruce.&nbsp;
{quote}\\
\\
\\

{color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford. ]]></property>
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<property name="body"><![CDATA[h1. Discussion of 18 Feb 2010

Luke Coletti, Doug Pargett, Jim Birch
# &nbsp;For July, 2010 WF cruise, ESP team will use Johnson lab 1Km housing.&nbsp; There were some issues with the last time it was used; weird readings--discussion ensued as to why readings not normal.
# Doug to draw up plans for pressure housing based on original aluminum design, keeping original diameter, using 2 radial o-rings to seal end caps.
# Doug will draw up plans for probe head opening using the actual probe he has, and getting rid of the current goofy SAE opening.
# We will make 2 Ti housings; ESP pays for 1, Johnson lab pays for 1.
# Eventually we will power the deep ISUS from our Deep-Sea Power and light battery stack, which will allow recharging if needed.&nbsp; But for July we'll use Luke's battery pack (especially since it's such a short deployment).\\

h1. ISUS specs

&nbsp;Based on Luke's LOBO experiences, one 'single stick' battery pack will power ISUS for 6 months if sampling once/hr.&nbsp; Thus, 20 min sampling rate would last \~1.2 months.&nbsp; Duration scales proportionally.
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:
{section}
{column}
!Logical Deployment Diagram.jpg|thumbnail,align=center!
{column}
{column:width=60%}
{panel:title=Things to note}
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.
{panel}
{column}
{section}


So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Data Import

{mockup:Data_Import|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] \- first discussion of adaptive sampling strategies
# Mar 3 - CMORE Hawaii
# [Mar 10] \-\- wand schematic
# [Mar 17]
# [Mar 24]
# Mar 31 - team deploying MOE at M0; Brent at WHOI
# [Apr 7]
# [Apr 14]
# [Apr 21]\--wand schematic reminder...
# [Apr 28]\--D-ESP 2-Year Birthday Celebration\!\!&nbsp; (Poster is [here|^ESP Birthday Poster(smaller).pdf])
# May 5 \-\- Visit to ASU
# [May 12]
# [May 19]]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]
# [Apr 12] \-\- Roman at WHOI, Chris P Europe
# Apr 19
# [Apr 26]
# [May 10]
# [May 17]]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 28]
# [Feb 4]
# [Mar 4]]]></property>
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<property name="body"><![CDATA[Present: Chris P., Bill, Jim, Chris S., John, Roman

Absent: Julie
\\

{color:#0033ff}1.&nbsp; Move ESP mtg time to accommodate CANON?{color}
* CANON meets every other Tuesday from 10-11.&nbsp; We will move ESP Science meeting.&nbsp; New time: 9-10am every Tuesday.&nbsp; Surface Commons.

{color:#0000ff}2.&nbsp; Updates:{color}
* Moe is in cold room and Chris will start running while Julie is on vacation this week.
* Puck giving blow-back, which allowed less and less reagent in.&nbsp; Roman has changed code and Bruce has run good DA's.&nbsp; Roman will move that code onto Mack (running latest Ruby) and see.&nbsp; ({color:#ff0000}3-4-10 update{color}:&nbsp; it works\!.&nbsp; Will use old DA code in new Ruby machines).
* Array printing.&nbsp; No message from Nilo, so unknown if cavro was installed this weekend.&nbsp; We will start printing with tips we have.
* Gordon reagents.&nbsp; It's set-up so it COULD run, but if we are serious, we should reload.&nbsp; Deemed lower priority given the S. Cal trip coming up.
* We should order more SPE columns.&nbsp; Addie ordered them last, lookup in PO's.&nbsp; We think from company called Column Engineering.

{color:#0000ff}3.&nbsp; MFB Traning?{color}
* There will be a training for water quality monitoring people in April after M0 deployment.&nbsp; SCCWRP, USC, MLML will each send 1 person.&nbsp; Stanford maybe 2 people.
* Purpose is introductory MFB training, then a referee session to determine who is doing what.
* Ali Boehm will get a COS post-doc that will come down for training.
* priority list on who gets MFB's is [here|ESPAPP:MFB-PCR distribution list|PCR distribution from MBARI].

{color:#0000ff}4.&nbsp; DA reagent schedule.{color}
* Chris S to check with Greg about DA production schedule.
* propose to get DA reagents March 23.{color:#0000ff}5.{color}{color:#0000ff}&nbsp;{color} {color:#0000ff}S. California deployment{color}
* no archiving during this deployment
* will take Shana Rae.  Use local divers.

]]></property>
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h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 15 Sep 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2015Sep08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[{mockup:testmock|2}

h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# 2009 Meeting Notes

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 15 Sep 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2015Sep08.pdf]
# [Engineering Timeline]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]

h2. Science

# [2008 Deployments]]]></property>
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<property name="body"><![CDATA[Present: Chris P., Bill, Jim, Chris S., John, Roman

Absent: Julie
\\

{color:#0033ff}1.&nbsp; Move ESP mtg time to accommodate CANON?{color}
* CANON meets every other Tuesday from 10-11.&nbsp; We will move ESP Science meeting.&nbsp; New time: 9-10am every Tuesday.&nbsp; Surface Commons.

{color:#0000ff}2.&nbsp; Updates:{color}
* Moe is in cold room and Chris will start running while Julie is on vacation this week.
* Puck giving blow-back, which allowed less and less reagent in.&nbsp; Roman has changed code and Bruce has run good DA's.&nbsp; Roman will move that code onto Mack (running latest Ruby) and see.&nbsp; ({color:#ff0000}3-4-10 update{color}:&nbsp; it works\!.&nbsp; Will use old DA code in new Ruby machines).
* Array printing.&nbsp; No message from Nilo, so unknown if cavro was installed this weekend.&nbsp; We will start printing with tips we have.
* Gordon reagents.&nbsp; It's set-up so it COULD run, but if we are serious, we should reload.&nbsp; Deemed lower priority given the S. Cal trip coming up.
* We should order more SPE columns.&nbsp; Addie ordered them last, lookup in PO's.&nbsp; We think from company called Column Engineering.

{color:#0000ff}3.&nbsp; MFB Traning?{color}
* There will be a training for water quality monitoring people in April after M0 deployment.&nbsp; SCCWRP, USC, MLML will each send 1 person.&nbsp; Stanford maybe 2 people.
* Purpose is introductory MFB training, then a referee session to determine who is doing what.
* Ali Boehm will get a COS post-doc that will come down for training.
* priority list on who gets MFB's is [here|ESPAPP:MFB-PCR distribution list|PCR distribution from MBARI].

{color:#0000ff}4.&nbsp; DA reagent schedule.{color}
* Chris S to check with Greg about DA production schedule.
* propose to get DA reagents March 23.{color:#0000ff}5.{color}{color:#0000ff}&nbsp;{color} {color:#0000ff}S. California deployment{color}
* no archiving during this deployment
* will take Shana Rae.  Use local divers.
* Discussion ensued about how to move instruments.&nbsp; Decided to have SR pick up mooring material on March 26.&nbsp; We drive two cans down on 30th and mount on 31st for April 1 deployment.]]></property>
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<property name="body"><![CDATA[See the new page I just added about parsing these entries on the context of the raw log file.


These entries may be defined any way you like

I don't see how "phases" can have names.&nbsp; A phase is a sequence of protocols.

Generally, the ESP sleeps between phases.&nbsp;

I like the  key=value format, but please try to shorten the key names a bit.  This log file is too big as it is.

I kind of like the idea of units suffixes, if you really intend to parse them.  But, if you are just going to ignore them,

I'd rather omit them entirely.  That means, the data manager has to know that 1L == 1000ml

Are you up for that?
\\]]></property>
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<property name="body"><![CDATA[In order to read in data from the ESP, the GUI will use the ESP's log file as the official 'interface' for data collection.  In order to facilitate this, this page documents what the entries in the log file should look like so that the ESP GUI will not have to make extensive and fragile rules to try and interpret the data.  The log entries should have the following format:

*\@EPOCH_SECONDS\@<*_Thread_*>ESPDM,*_EVENT-NAME_*,*_attribute=value,..._

Notes:
# Time is designated using epoch seconds (number of seconds that have elapsed since January 1, 1970) in _GMT_
# EVENT_NAME is one of the following:
## BEGIN_MISSON
## PHASE_START
## PHASE_END
## PROTOCOL_START
## PROTOCOL_END
## SAMPLE_START
## SAMPLE_END
## CAMERA_SNAP
## END_MISSION
# Attributes are key=value pairs and vary from event to event.  Attributes for the various events are:
## BEGIN_MISSON
### No attributes
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,BEGIN_MISSION}}
## PHASE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,PHASE_START,phase_name=hab}}
## PHASE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ (this is the time that the phase started.  This is necessary due to the fact there are multiple threads the name & start date are the unique key.)
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,PHASE_END,phase_name=hab,phase_start=2008-11-10T15:34:23-8}}
## PROTOCOL_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=YYYYY (e.g. sh1, sh2, wcr)
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,PROTOCOL_START,phase_name=hab,phase_start=2008-11-10T15:34:23-8,protocol_name=sh1}}
## PROTOCOL_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=YYYYY (e.g. sh1, sh2, wcr)
### protocol_start=YYYY-MM-DDThh:mm:ssZ
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,PROTOCOL_END,phase_name=hab,phase_start=2008-11-10T15:34:23-8,protocol_name=sh1,protocol_start=2008-11-10T15:34:23-8}}
## SAMPLE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=YYYYY (e.g. sh1, sh2, wcr)
### protocol_start=YYYY-MM-DDThh:mm:ssZ
### target_volume=ZZZZml
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,SAMPLE_START,phase_name=hab,phase_start=2008-11-10T15:34:23-8,protocol_name=sh1,protocol_start=2008-11-10T15:34:23-8,target_volume=1000ml}}
## SAMPLE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=YYYYY (e.g. sh1, sh2, wcr)
### protocol_start=YYYY-MM-DDThh:mm:ssZ
### sample_volume=ZZZZml
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,SAMPLE_END,phase_name=hab,phase_start=2008-11-10T15:34:23-8,protocol_name=sh1,protocol_start=2008-11-10T15:34:23-8,sample_volume=934.1ml}}
## CAMERA_SNAP
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### file_name=ZZZZZZZZZ.tif
### auto_exposure=AAAAAAAs
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,CAMERA_SNAP,phase_name=hab,phase_start=2008-11-10T15:34:23-8,file_name=bac08oct1716h450ml40s.tif,auto_exposure=123.4s}}
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<property name="body"><![CDATA[In order to read in data from the ESP, the GUI will use the ESP's log file as the official 'interface' for data collection.  In order to facilitate this, this page documents what the entries in the log file should look like so that the ESP GUI will not have to make extensive and fragile rules to try and interpret the data.  The log entries should have the following format:

*@EPOCH_SECONDS@<*_Thread_*>ESPDM,*_EVENT-NAME_*,*_attribute=value,..._

Notes:
# Time is designated using epoch seconds (number of seconds that have elapsed since January 1, 1970) in _GMT_
# EVENT_NAME is one of the following:
## BEGIN_MISSON
## PHASE_START
## PHASE_END
## PROTOCOL_START
## PROTOCOL_END
## SAMPLE_START
## SAMPLE_END
## CAMERA_SNAP
## END_MISSION
# Attributes are key=value pairs and vary from event to event.  Attributes for the various events are:
## BEGIN_MISSON
### No attributes
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,BEGIN_MISSION}}
## PHASE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,PHASE_START,phase_name=hab}}
## PHASE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ (this is the time that the phase started.  This is necessary due to the fact there are multiple threads the name & start date are the unique key.)
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,PHASE_END,phase_name=hab,phase_start=2008-11-10T15:34:23-8}}
## PROTOCOL_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=YYYYY (e.g. sh1, sh2, wcr)
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,PROTOCOL_START,phase_name=hab,phase_start=2008-11-10T15:34:23-8,protocol_name=sh1}}
## PROTOCOL_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=YYYYY (e.g. sh1, sh2, wcr)
### protocol_start=YYYY-MM-DDThh:mm:ssZ
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,PROTOCOL_END,phase_name=hab,phase_start=2008-11-10T15:34:23-8,protocol_name=sh1,protocol_start=2008-11-10T15:34:23-8}}
## SAMPLE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=YYYYY (e.g. sh1, sh2, wcr)
### protocol_start=YYYY-MM-DDThh:mm:ssZ
### target_volume=ZZZZml
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,SAMPLE_START,phase_name=hab,phase_start=2008-11-10T15:34:23-8,protocol_name=sh1,protocol_start=2008-11-10T15:34:23-8,target_volume=1000ml}}
## SAMPLE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=YYYYY (e.g. sh1, sh2, wcr)
### protocol_start=YYYY-MM-DDThh:mm:ssZ
### sample_volume=ZZZZml
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,SAMPLE_END,phase_name=hab,phase_start=2008-11-10T15:34:23-8,protocol_name=sh1,protocol_start=2008-11-10T15:34:23-8,sample_volume=934.1ml}}
## CAMERA_SNAP
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### file_name=ZZZZZZZZZ.tif
### auto_exposure=AAAAAAAs
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,CAMERA_SNAP,phase_name=hab,phase_start=2008-11-10T15:34:23-8,file_name=bac08oct1716h450ml40s.tif,auto_exposure=123.4s}}
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<property name="body"><![CDATA[In order to read in data from the ESP, the GUI will use the ESP's log file as the official 'interface' for data collection.  In order to facilitate this, this page documents what the entries in the log file should look like so that the ESP GUI will not have to make extensive and fragile rules to try and interpret the data.  The log entries should have the following format:

*@*_YYYY_\-_MM_\-_DD_*T*_HH_*:*_mm_*:*_ssZ_*@<*_Thread_*>ESPDM,*_EVENT-NAME_*,*_attribute=value,..._

Notes:
# Time designation is the ISO 8601 timestamp ([http://en.wikipedia.org/wiki/ISO_8601])
# hh = hours and is 24 hour clock
# Z is timezone and can be specified as Z for UTC or an offset from UTC with \+_hh:mm
# EVENT_NAME is one of the following:
## BEGIN_MISSON
## PHASE_START
## PHASE_END
## PROTOCOL_START
## PROTOCOL_END
## SAMPLE_START
## SAMPLE_END
## CAMERA_SNAP
## END_MISSION
# Attributes are key=value pairs and vary from event to event.  Attributes for the various events are:
## BEGIN_MISSON
### No attributes
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,BEGIN_MISSION}}
## PHASE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,PHASE_START,phase_name=hab}}
## PHASE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ (this is the time that the phase started.  This is necessary due to the fact there are multiple threads the name & start date are the unique key.)
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,PHASE_END,phase_name=hab,phase_start=2008-11-10T15:34:23-8}}
## PROTOCOL_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=YYYYY (e.g. sh1, sh2, wcr)
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,PROTOCOL_START,phase_name=hab,phase_start=2008-11-10T15:34:23-8,protocol_name=sh1}}
## PROTOCOL_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=YYYYY (e.g. sh1, sh2, wcr)
### protocol_start=YYYY-MM-DDThh:mm:ssZ
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,PROTOCOL_END,phase_name=hab,phase_start=2008-11-10T15:34:23-8,protocol_name=sh1,protocol_start=2008-11-10T15:34:23-8}}
## SAMPLE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=YYYYY (e.g. sh1, sh2, wcr)
### protocol_start=YYYY-MM-DDThh:mm:ssZ
### target_volume=ZZZZml
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,SAMPLE_START,phase_name=hab,phase_start=2008-11-10T15:34:23-8,protocol_name=sh1,protocol_start=2008-11-10T15:34:23-8,target_volume=1000ml}}
## SAMPLE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=YYYYY (e.g. sh1, sh2, wcr)
### protocol_start=YYYY-MM-DDThh:mm:ssZ
### sample_volume=ZZZZml
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,SAMPLE_END,phase_name=hab,phase_start=2008-11-10T15:34:23-8,protocol_name=sh1,protocol_start=2008-11-10T15:34:23-8,sample_volume=934.1ml}}
## CAMERA_SNAP
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### file_name=ZZZZZZZZZ.tif
### auto_exposure=AAAAAAAs
### Example: {{@2008-11-10T15:34:23-8@<Main>ESPDM,CAMERA_SNAP,phase_name=hab,phase_start=2008-11-10T15:34:23-8,file_name=bac08oct1716h450ml40s.tif,auto_exposure=123.4s}}
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<property name="body"><![CDATA[In order to read in data from the ESP, the GUI will use the ESP's log (*real.log*) file as the official 'interface' for data collection.  In order to facilitate this, this page documents what the entries in the log file should look like so that the ESP GUI will not have to make extensive and fragile rules to try and interpret the data.  The log entries should have the following format:

*\@EPOCH_SECONDS\@<*_Thread_*>DATAMGMT,*_EVENT-NAME_*,*_attribute=value,..._

Notes:
# Time is designated using epoch seconds (number of seconds that have elapsed since January 1, 1970) in _GMT_
# EVENT_NAME is one of the following:
## BEGIN_MISSON
## PHASE_START
## PHASE_END
## PROTOCOL_START
## PROTOCOL_END
## SAMPLE_START
## SAMPLE_END
## CAMERA_SNAP
## END_MISSION
# Attributes are key=value pairs and vary from event to event.  Attributes for the various events are:
## BEGIN_MISSON
### No attributes
### Example: {{@1231372399@<Main>DATAMGMT,BEGIN_MISSION}}
## PHASE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### Example: {{@1231372399@<Main>DATAMGMT,PHASE_START,phase_name=hab}}
## PHASE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS (this is the time that the phase started.  This is necessary due to the fact there are multiple threads the name & start date are the unique key.)
### Example: {{@1231372399@<Main>DATAMGMT,PHASE_END,phase_name=hab,phase_start=1231372399}}
## PROTOCOL_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECDONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### Example: {{@1231372399@<Main>DATAMGMT,PROTOCOL_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1}}
## PROTOCOL_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### Example: {{@1231372399@<Main>DATAMGMT,PROTOCOL_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399}}
## SAMPLE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### target_volume=ZZZZml
### Example: {{@1231372399@<Main>DATAMGMT,SAMPLE_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,target_volume=1000ml}}
## SAMPLE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### sample_volume=ZZZZml
### Example: {{@1231372399@<Main>DATAMGMT,SAMPLE_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,sample_volume=934.1ml}}
## CAMERA_SNAP
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### file_name=ZZZZZZZZZ.tif
### auto_exposure=AAAAAAAs
### Example: {{@1231372399@<Main>DATAMGMT,CAMERA_SNAP,phase_name=hab,phase_start=1231372399,file_name=bac08oct1716h450ml40s.tif,auto_exposure=123.4s}}
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<property name="body"><![CDATA[In order to read in data from the ESP, the GUI will use the ESP's log file as the official 'interface' for data collection.  In order to facilitate this, this page documents what the entries in the log file should look like so that the ESP GUI will not have to make extensive and fragile rules to try and interpret the data.  The log entries should have the following format:

*\@EPOCH_SECONDS\@<*_Thread_*>DATAMGMT,*_EVENT-NAME_*,*_attribute=value,..._

Notes:
# Time is designated using epoch seconds (number of seconds that have elapsed since January 1, 1970) in _GMT_
# EVENT_NAME is one of the following:
## BEGIN_MISSON
## PHASE_START
## PHASE_END
## PROTOCOL_START
## PROTOCOL_END
## SAMPLE_START
## SAMPLE_END
## CAMERA_SNAP
## END_MISSION
# Attributes are key=value pairs and vary from event to event.  Attributes for the various events are:
## BEGIN_MISSON
### No attributes
### Example: {{@1231372399@<Main>DATAMGMT,BEGIN_MISSION}}
## PHASE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### Example: {{@1231372399@<Main>DATAMGMT,PHASE_START,phase_name=hab}}
## PHASE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS (this is the time that the phase started.  This is necessary due to the fact there are multiple threads the name & start date are the unique key.)
### Example: {{@1231372399@<Main>DATAMGMT,PHASE_END,phase_name=hab,phase_start=1231372399}}
## PROTOCOL_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECDONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### Example: {{@1231372399@<Main>DATAMGMT,PROTOCOL_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1}}
## PROTOCOL_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### Example: {{@1231372399@<Main>DATAMGMT,PROTOCOL_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399}}
## SAMPLE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=YYYY-MM-DDThh:mm:ssZ
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### target_volume=ZZZZml
### Example: {{@1231372399@<Main>DATAMGMT,SAMPLE_START,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,target_volume=1000ml}}
## SAMPLE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### protocol_name=PPPPP (e.g. sh1, sh2, wcr)
### protocol_start=EPOCH_SECONDS
### sample_volume=ZZZZml
### Example: {{@1231372399@<Main>DATAMGMT,SAMPLE_END,phase_name=hab,phase_start=1231372399,protocol_name=sh1,protocol_start=1231372399,sample_volume=934.1ml}}
## CAMERA_SNAP
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### phase_start=EPOCH_SECONDS
### file_name=ZZZZZZZZZ.tif
### auto_exposure=AAAAAAAs
### Example: {{@1231372399@<Main>DATAMGMT,CAMERA_SNAP,phase_name=hab,phase_start=1231372399,file_name=bac08oct1716h450ml40s.tif,auto_exposure=123.4s}}
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<property name="body"><![CDATA[Present:
Absent: , Addie (maternity)

h3.


h3. Machine Builds

* &nbsp;

h3. MFB

* &nbsp;

h3. Software

* &nbsp;

h3. DWSM


h6. +Sphere+

* &nbsp;

h6. +Elevator+

* &nbsp;

*{+}DWSM{+}*
* &nbsp;

h3. GUI Development

* &nbsp;

h3. Other Items:

* &nbsp;]]></property>
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<property name="body"><![CDATA[Software Revision level for Instrument Betty
OS
 1 March 2010 Version 1.8 by Brent
Ruby
Protocol
Sleepy Firmware
Sleepy CPLD
Core Firmware
Core CPLD
RValve CPLD]]></property>
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<property name="body"><![CDATA[Present: Jim, Chris S., Wayne, Brent, Doug, Cheri, Scott, Jose
Absent: , Addie (maternity)

h3.


h3. Machine Builds

* &nbsp;Two new cores are being kitted by Cheri.
* Syringe and rotary valve parts were inadvertently left off original (July) El Camino order.&nbsp; Mike P. pushing those through and should be ready by Jan 23.
* Discussion on McLane visit for core builds.&nbsp; Decided to have them reserve 2 weeks; Feb 8 and Feb 22.&nbsp; If they really work the first week, maybe stay longer and make it just one trip out.
* Cheri has drawing of new harmonic drive mount.&nbsp; We need it manufactured.&nbsp; Will talk to Mark Brown about getting some (Non-Mike Parker) help.
* Cold syringe testing.&nbsp; Not finished.&nbsp; Deadline is when we put a core in the sphere (late March).
* Next two Sleepy core boards need names.&nbsp; Cheri will spearhead that effort.

h3. MFB

* &nbsp;

h3. Software

* &nbsp;

h3. DWSM


h6. +Sphere+

* &nbsp;All connectors are in for the sphere.&nbsp; We will move it to Bellingham AUV lab Monday for install.&nbsp; Plan is still to get it shipped to SRI late next week.
* Decision is to ship it *{+}disassembled{+}*.

h6. +Elevator+

* &nbsp;Mike Parker waiting for solidmodel from Doug.&nbsp; Will send today.
* Currently, elevator has no legs.&nbsp; Doug has designed 6 8" standing legs, and 3 adjustable legs for ocean bottom landings.
* Adjustable legs being&nbsp; designed for up to 20 degree slope.
* Jim will talk to Mark Brown about getting Mike Conway help on drop-weight design.

*{+}DWSM{+}*
* &nbsp;Mechanically, DWSM is 95% complete.
* Software interface still needs design and many electrical connectors/cables to order.&nbsp; Brent and Scott are on it.&nbsp; They will meet with Doug to create config file that is usable for testing.

h3. GUI Development

* &nbsp;

h3. Other Items:

* &nbsp;]]></property>
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<property name="body"><![CDATA[h3. &nbsp;Machine Builds

* Bruce has been run a lot and can't reproduce the processing error
* Seems to be an accumulation of something in the software (27May\--happening on Neo during deployment-\-more evidence it's software and not dwarf)
* HANDS
** Gordon's goes at 50% force (old ones worked at 30%)
** Betty taking 70% but with new frame works better than Gordon.

h3. MFB


h3. Drifter

* Test tank tomorrow (Friday).
* Dive days moved to 27 and 28 next week. Likely will only use the 27th.
* There will be no tension control on winch for June dive.
* Pressure transducer and moxa need mounting on lid
** need fitting and adaptor using power port on lid
** Mike P to make bracket for MOXA
** Roman to move mooring to high bay; Jim to get Ken Smith batteries
* Gene wants ESP 100lbs negative.&nbsp; Will work with Mike to accomplish.
* BRUCE is going in drifter

h3. Software

* &nbsp;

h3. Deep ESP


h6.

* Wand; don't have cables long enough for long wand assembly.&nbsp; Cables arrive 29th (too late)
* Will shoot for a 3' stubby.&nbsp; Code still to be developed
* TSV--needed tightening
* CPLD code works but needs testing
* Mink is soldered and waiting for modem before potting.
* D-ESP cleaning
** Doug has two 4" sections that can't be cleaned with toxicant.&nbsp; So idea is to add a filter puck taht we push tox through the core to clean both those lines in DWSM, then go to next SH1 run.

h3. GUI

* Will be loaded on Gordon and Betty for beta testing.

h3. Deployment Issues

For June:
* Mack in sphere
* Bruce in Drifter
* Moe on bench

h1. \\
*September/October Mack and Bruce 2009*



h6. &nbsp; &nbsp; * See attachments for deployment calendar &nbsp;


h6. &nbsp;&nbsp;&nbsp; * If the code needs to be tweeked to use the V2 ctd or one surface ESP will not have a CTD


h6. &nbsp; &nbsp; * we need larger battery pack for ISUS to get high density sampling endurance


h6. &nbsp;&nbsp;&nbsp; * need to get dry and wet weight of drifter base before I put it back to standard


h6. &nbsp; &nbsp; * ESP and Iridium batteries



h3. &nbsp;Other Items:

* need loaner computer from IS for summer student&nbsp; (Cheri will put in request with IS for what we need)
Here is the schedule for the next two weeks:

* {gliffy:name=calendar\|space=ESPAPP\|page=21May2009\|pageid=10354699\|align=left\|size=L}
* 09may27=>&nbsp; There is water in one of the floats on the bail of the base used for the drifter.&nbsp; Need to check and drain before a shallow deployment of that base.]]></property>
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<property name="body"><![CDATA[h3. Machine Builds

* Bruce has been run a lot and can't reproduce the processing error
* Seems to be an accumulation of something in the software (27May\--happening on Neo during deployment-\-more evidence it's software and not dwarf)
* HANDS
** Gordon's goes at 50% force (old ones worked at 30%)
** Betty taking 70% but with new frame works better than Gordon.

h3. MFB


h3. Drifter

* Test tank tomorrow (Friday).
* Dive days moved to 27 and 28 next week. Likely will only use the 27th.
* There will be no tension control on winch for June dive.
* Pressure transducer and moxa need mounting on lid
** need fitting and adaptor using power port on lid
** Mike P to make bracket for MOXA
** Roman to move mooring to high bay; Jim to get Ken Smith batteries
* Gene wants ESP 100lbs negative.&nbsp; Will work with Mike to accomplish.
* BRUCE is going in drifter

h3. Software

* &nbsp;

h3. Deep ESP


h6.

* Wand; don't have cables long enough for long wand assembly.&nbsp; Cables arrive 29th (too late)
* Will shoot for a 3' stubby.&nbsp; Code still to be developed
* TSV--needed tightening
* CPLD code works but needs testing
* Mink is soldered and waiting for modem before potting.
* D-ESP cleaning
** Doug has two 4" sections that can't be cleaned with toxicant.&nbsp; So idea is to add a filter puck taht we push tox through the core to clean both those lines in DWSM, then go to next SH1 run.

h3. GUI

* Will be loaded on Gordon and Betty for beta testing.

h3. Deployment Issues

For June:
* Mack in sphere
* Bruce in Drifter
* Moe on bench&nbsp;

\\
\\
\\

h3. &nbsp;Other Items:

* need loaner computer from IS for summer student&nbsp; (Cheri will put in request with IS for what we need)
Here is the schedule for the next two weeks:

* {gliffy:name=calendar\|space=ESPAPP\|page=21May2009\|pageid=10354699\|align=left\|size=L}
* 09may27=>&nbsp; There is water in one of the floats on the bail of the base used for the drifter.&nbsp; Need to check and drain before a shallow deployment of that base.]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. &nbsp;


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]
# [Feb 16]]]></property>
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</property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]
# [Feb 16]
# Feb 23 \-\- Oceans, Portland
# [Mar 2]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">11240242</id>
</property>
</object>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]

h2. Science


# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [MFB/PCR distribution list] as of 03Mar2010]]></property>
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<id name="id">11272988</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]

h2. Science

## [MFB/PCR distribution list]
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]
Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Data Import

{mockup:Data_Import|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



]]></property>
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<property name="body"><![CDATA[In order to read in data from the ESP, the GUI will use the ESP's log file as the official 'interface' for data collection.  In order to facilitate this, this page documents what the entries in the log file should look like so that the ESP GUI will not have to make extensive and fragile rules to try and interpret the data.  The log entries should have the following format:

@YYYY-MM-DDThh:mm:ssZ@<Thread>ESPDM,EVENT_NAME,attribute=value,...

Notes:
# Log file should start with an entry that signifies that it has the ESPDM entries in it to separate from old style.
# Time designation is the ISO 8601 timestamp (http://en.wikipedia.org/wiki/ISO_8601)
# hh = hours and is 24 hour clock
# Z is timezone and can be specified as Z for UTC or an offset from UTC with +_hh:mm
# EVENT_NAME is one of the following:
## PHASE_START
## PHASE_END
## PROTOCOL_START
## PROTCOL_END
## SAMPLE_START
## SAMPLE_END
## CAMERA_SNAP
# Attributes are key=value pairs and vary from event to event.  Attributes for the various events are:
## PHASE_START
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
## PHASE_END
### phase_name=XXXXXX (e.g. hab, larv, da, habda)
### started_at=YYYY-MM-DDThh:mm:ssZ (this is the time that the phase started.  This is necessary due to the fact there are multiple threads the name & start date are the unique key.)
###  ]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:

&nbsp; !Logical Deployment Diagram.jpg|thumbnail,align=center!
Some things to note about this diagram:
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.

So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

Below is a mockup of what the user might see upon first starting the application.
{mockup:Top Level|12}

Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?

Here is the mockup showning what might happen if the user selected on of the instruments.
{mockup:InstrumentSelect|3}

After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times

A mockup of this view is show here:
{mockup:DeploymentSelect|3}

In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open. This is shown in the following mockups

{mockup:MouseOverEvent|2}

{mockup:EventDetails|2}

There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Data Import

{mockup:Data_Import|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar] (note to run this, open a command prompt and type java -jar esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar)

h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]

h3. Project Documentation:
# [Requirements (and Gathering)|Requirements (and Gathering) Documentation]
# [Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]

]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]

h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]

h3. Project Documentation:
# [Requirements (and Gathering)|Requirements (and Gathering) Documentation]
# [Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]

]]></property>
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'java -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will start the application

h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]

h3. Project Documentation:
# [Requirements (and Gathering)|Requirements (and Gathering) Documentation]
# [Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]

]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]
# [04Sep2008]
# [11Sep2008]
# [18Sep2008]
# [25Sep2008]
# [02Oct2008] (Pre-deployment discussions)
# [09Oct2008] (the day after deployment....)
# [16Oct2008]
# [23Oct2008]
# [30Oct2008]
# [06Nov2008]]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision
# [25Jun2009]
# 02Jul2009 -- no meeting; 4th of July break
# [09Jul2009]
# [16Jul2009]
# [23Jul2009]
# 30Jul2009 -- Scott ran mtg; proposal preparation
# [06Aug2009]]]></property>
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<property name="body"><![CDATA[Software Revision level for Instrument Betty
OS
Ruby
Protocol
Firmware]]></property>
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<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically+

April 6--Bruce at M0 for surface deployment (Zephyr)

April 15--Mack in Sphere for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

April 29--Recover Bruce at M0 (Zephyr)

May 1--Mack in sphere connected to DWSM(dive #3); incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

May 14--Deploy NEO w/PCR, surface deployment (Zephyr)

May 27--First Drifter dive (Zephyr)

June 5-9 \-\- Western Flyer.&nbsp; D-ESP, Drifter, and CTD casts. {color:#cc0000}{*}MOVIES{*}{color}:  D-ESP launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/DESP%20deployment%20(full%20quality).dv].  Drifter launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/Drifter.dv].

June 11 \-\- Recover NEO.&nbsp; (Zephyr)

]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]
# [04Sep2008]
# [11Sep2008]
# [18Sep2008]
# [25Sep2008]
# [02Oct2008] (Pre-deployment discussions)
# [09Oct2008] (the day after deployment....)
# [16Oct2008]
# [23Oct2008]
# [30Oct2008]
# [06Nov2008]
# [13Nov2008]
# [20Nov2008] (Scott's in charge)]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]
# [04Sep2008]
# [11Sep2008]
# [18Sep2008]
# [25Sep2008]
# [02Oct2008] (Pre-deployment discussions)
# [09Oct2008] (the day after deployment....)
# [16Oct2008]]]></property>
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<property name="body"><![CDATA[# [03Jan2008]
# [10Jan2008]
# [17Jan2008]
# [24Jan2008]
# [31Jan2008]
# [07Feb2008]
# [14Feb2008]
# [21Feb2008]
# [28Feb2008]
# [06Mar2008]
# [13Mar2008 (Teleconference with LLNL)]
# [20Mar2008]
# [27Mar2008 (Pre-deployment mtg)]
# 03Apr2008 (no mtg--1st Mack deployment)
# [10Apr2008]
# [17Apr2008]
# [24Apr2008]
# 1May2008 (no mtg-2nd Mack deployment)
# [8May2008]
# 15May2008 (no mtg-Bruce swap for Mack deployment)
# [22May2008]
# [30May2008 (Moved to Friday)]
# [5Jun2008]
# [12Jun2008]
# [10Jul2008]
# [17Jul2008]
# [25Jul2008] (Moved to Friday due to McLane visit)
# [31Jul2008]
# [07Aug2008]
# [21Aug2008]
# [28Aug2008]
# [04Sep2008]
# [11Sep2008]
# [18Sep2008]
# [25Sep2008]
# [02Oct2008] (Pre-deployment discussions)
# [09Oct2008] (the day after deployment....)
# [16Oct2008]
# [23Oct2008]
# [30Oct2008]
# [06Nov2008]
# [13Nov2008]]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument and the various places it will live.  The ESP directory structures contains the following:

# /var/log on the linux host is the root directory for the FTP site (i.e. = ftp://espName).
# /var/log/messages contains linux kernel messages
# /var/log/vsftpd.log records all FTP site traffic
# /var/log/$USER is top level output directory for each user's ESP data (can be overridden with $ESPlog variable, but this is rare)
# Content in /var/log depends on configuration, but default is:
## _hires_: high resolution camera images (each approx 3.5 MB)
## _lores_: low resolution camera images
## _midres_: medium resolution camera images (typically autoexposures)
## Top level directory contains default resolution camera images (typically fixed exposures)
# Only files in top level directory are uploaded to shore
# File types are:
## *.tif = TIFF camera images
## *.pcr = Comma Separated Value PCR Data
## *.out = Console output capture
### Text normally output to the esp interactive console
### Redirected here when running non-interactive mission script
### Can be viewed with showlog command
### File is named after operating mode (real, sim, simreal, quick)
## *.log = detailed, binary esp engineering logs.  The file is named after operating mode (real, sim, simreal, quick).  Can be viewed with dumplog.
## *.tube = list of carousel tubes processed
### One tube per line, last line is the currently active source tube
## ISUS*.err = ISUS error messages (direct from the ISUS)
## ISUS*.dat = text records of the ISUS data (complex and incorporates CTD data)
## CTD*.hex = CTD data in hexidecimal formatted text records
### Seabird specific format

A diagram of that structure is shown here:
{section}
{column}
{gliffy:name=ESP Data Overview|space=ESPAPP|page=Design|pageid=6258757|align=left|size=M}
{column}
{column:width=60%}
{panel:title=Things to note}
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station (this includes the ruby scripts used to run the ESP).
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.
{panel}
{column}
{section}


So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

So, in order to manage this synchronization and storage of data, it was decided that the GUI would be reponsible for that synchronization.  Initially it would be a manual process as it will be time consuming and the user should be responsible for firing it off.  Then, once it is solidified a bit, it would be nice to push it back to a background thread that happens automatically.  The GUI for this synchronization, might look something like this:

{mockup:Data_Import|1}


Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

||Mockup||Notes||
|{mockup:Top Level|12}|A mockup of what the user might see upon first starting the application.|
|{mockup:InstrumentSelect|3}|Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?
Here is the mockup showing what might happen if the user selected one of the instruments.|
|{mockup:DeploymentSelect|3}|After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times|
|{mockup:MouseOverEvent|2}\\{mockup:EventDetails|2}|In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open.|




There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument and the various places it will live.  The ESP directory structures contains the following:

# /var/log on the linux host is the root directory for the FTP site (i.e. = ftp://espName).
# /var/log/messages contains linux kernel messages
# /var/log/vsftpd.log records all FTP site traffic
# /var/log/$USER is top level output directory for each user's ESP data (can be overridden with $ESPlog variable, but this is rare)
# Content in /var/log depends on configuration, but default is:
## _hires_: high resolution camera images (each approx 3.5 MB)
## _lores_: low resolution camera images
## _midres_: medium resolution camera images (typically autoexposures)
## Top level directory contains default resolution camera images (typically fixed exposures)
# Only files in top level directory are uploaded to shore
# File types are:
## *.tif = TIFF camera images
## *.pcr = Comma Separated Value PCR Data
## *.out = Console output capture
### Text normally output to the esp interactive console
### Redirected here when running non-interactive mission script
### Can be viewed with showlog command
### File is named after operating mode (real, sim, simreal, quick)
## *.log = detailed, binary esp engineering logs.  The file is named after operating mode (real, sim, simreal, quick).  Can be viewed with dumplog.
## *.tube = list of carousel tubes processed
### One tube per line, last line is the currently active source tube
## ISUS*.err = ISUS error messages (direct from the ISUS)
## ISUS*.dat = text records of the ISUS data (complex and incorporates CTD data)
## CTD*.hex = CTD data in hexidecimal formatted text records
### Seabird specific format

The initial thought about how a complete data management system might look is:
{section}
{column}
{gliffy:name=ESP Data Overview|space=ESPAPP|page=Design|pageid=6258757|align=left|size=M}
{column}
{column:width=60%}
{panel:title=Things to note}
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station (this includes the ruby scripts used to run the ESP).
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.
{panel}
{column}
{section}


So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

So, in order to manage this synchronization and storage of data, it was decided that the GUI would be reponsible for that synchronization.  Initially it would be a manual process as it will be time consuming and the user should be responsible for firing it off.  Then, once it is solidified a bit, it would be nice to push it back to a background thread that happens automatically.  The GUI for this synchronization, might look something like this:

{mockup:Data_Import|1}


Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

||Mockup||Notes||
|{mockup:Top Level|12}|A mockup of what the user might see upon first starting the application.|
|{mockup:InstrumentSelect|3}|Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?
Here is the mockup showing what might happen if the user selected one of the instruments.|
|{mockup:DeploymentSelect|3}|After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times|
|{mockup:MouseOverEvent|2}\\{mockup:EventDetails|2}|In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open.|




There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process:

h3. Requirements
||Number||Requirement||Associated View||
|1|User can define missions by specifying phases|Planning|
|2|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|Be able to add non-phase/protocol events (user defined) to the calendar anywhere|Operation|
|5|Be able to set mission start end times that are not associated with a phase/protocol|Planning|
|6|Be able to specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User shall be able to add comments to a phase that will be generated in the script|Planning|
|8|User shall be able to view images associated with phases|Operation|
|9|User shall be able to browse the .GAL file along with image and filter paper information|Operation|
|10|User should be able to browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Operation|
|11|User should be able to browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Operation|
|12|User should be able to associate external files with events (excel spreadsheet, documents, etc.)|Planning,Operation|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|Operation|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users should have a form to add/delete/edit protocol runs and phases|Planning|
|16|Users should have a form to add/delete/edit consumables|Planning|
|17|In application users should have sample volume listed with protocol run|Planning|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should somehow be shown|Operation|
|19|Tide and phase information should be available during planning|Planning,Operation|
|20|Application should allow for details of flushes to be seen/accounted for|Operation|
|21|Users should be able to schedule Kills (end purges) or disable kills|Planning|
|22|Users should be able to define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to download instrument logs and images and the GUI will parse out the following events: 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time|Operation|
|24|Users should be able to visualize the current state of the instrument|Operation,State|
|25|Users should be able to scroll back in time and visualize instrument state at the various points in time|State|

h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from User Manual Meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual Meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument and the various places it will live.  That diagram is shown here:
{section}
{column}
{gliffy:name=ESP Data Overview|space=ESPAPP|page=Design|pageid=6258757|align=left|size=M}
{column}
{column:width=60%}
{panel:title=Things to note}
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station (this includes the ruby scripts used to run the ESP).
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.
{panel}
{column}
{section}


So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

So, in order to manage this synchronization and storage of data, it was decided that the GUI would be reponsible for that synchronization.  Initially it would be a manual process as it will be time consuming and the user should be responsible for firing it off.  Then, once it is solidified a bit, it would be nice to push it back to a background thread that happens automatically.  The GUI for this synchronization, might look something like this:

{mockup:Data_Import|1}


Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

||Mockup||Notes||
|{mockup:Top Level|12}|A mockup of what the user might see upon first starting the application.|
|{mockup:InstrumentSelect|3}|Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?
Here is the mockup showing what might happen if the user selected one of the instruments.|
|{mockup:DeploymentSelect|3}|After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times|
|{mockup:MouseOverEvent|2}\\{mockup:EventDetails|2}|In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open.|




There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



]]></property>
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process:

h3. Requirements
||Number||Requirement||Associated View||
|1|User can define missions by specifying phases|Planning|
|2|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|Be able to add non-phase/protocol events (user defined) to the calendar anywhere|Operation|
|5|Be able to set mission start end times that are not associated with a phase/protocol|Planning|
|6|Be able to specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User shall be able to add comments to a phase that will be generated in the script|Planning|
|8|User shall be able to view images associated with phases|Operation|
|9|User shall be able to browse the .GAL file along with image and filter paper information|Operation|
|10|User should be able to browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Operation|
|11|User should be able to browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Operation|
|12|User should be able to associate external files with events (excel spreadsheet, documents, etc.)|Planning,Operation|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|Operation|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users should have a form to add/delete/edit protocol runs and phases|Planning|
|16|Users should have a form to add/delete/edit consumables|Planning|
|17|In application users should have sample volume listed with protocol run|Planning|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should somehow be shown|Operation|
|19|Tide and phase information should be available during planning|Planning,Operation|
|20|Application should allow for details of flushes to be seen/accounted for|Operation|
|21|Users should be able to schedule Kills (end purges) or disable kills|Planning|
|22|Users should be able to define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to download instrument logs and images and the GUI will parse out the following events: 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time|Operation|
|24|Users should be able to visualize the current state of the instrument|Operation,State|
|25|Users should be able to scroll back in time and visualize instrument state at the various points in time|State|

h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[Present: Scott, Doug, Chris S., Kevin, Jim, Cheri, Brent, Wayne
Absent:&nbsp; Addie (SolidWorks training)

h3.


h3. Machine Builds

* &nbsp;Scott wants to change power connectors on our 3 surface cans; current ones are starting to break.&nbsp; Total of $4K.&nbsp; Yes, we will do--charging to 900612.
* Moe finished with pressure calibration.&nbsp; Fluid has been moved through the core.&nbsp; All that's left is temperature calibration (cold, room, hot) which should take 2 days.
* {color:#3300ff}We must add '{color}{color:#3300ff}{*}{+}light{+}{*}{color} {color:#3300ff}{*}puck{*}{color} {color:#3300ff}checkout' to our checkout procedure to help understand camera variability.{color}
* {color:#000000}must change O-ring material--cracks discovered on Moe's o-rings, where no fluids have been run.&nbsp; Will got to Viton or Silicon.{color}

h3. MFB

* &nbsp;Writing schematic for MFB is turning out to be more difficult than first thought because of prior documentation.&nbsp; Scott working to fix the mess.
* MFB valve problem that stopped our dye testing yesterday turns out to be a wrong valve assignment.&nbsp; Unclear how assigment got changed, but Scott to track down.
* Jim will talk to Jose about having parts ready for Addie's McLane build.&nbsp; Jose gone the month of December, and we need 2 wiring harnesses, 2 voltage regulators, 1 I2C power board before he leaves.
* Question came up as to how close the grill is for niave user (Kendra) to start pushing fluids and do a basic checkout.&nbsp; Must call Addie.

h3. Software

* &nbsp;Debugging on Neo is running, but so far no problems.&nbsp; It is running all contextual sensors, but one difference with deployment is that is running on the network, not locally.&nbsp; Reason for this was....
* Also, small change to the Ruby interpreter was installed that now releases dead stacks, so it doesn't try to chase any dead references.&nbsp; This may have fixed our problem.
* All NEO software will be merged back in the main trunk, which may cause problems for Bruce and Mack.&nbsp; Since these two are going to be run hard, Brent should check with Chris before this merger takes place.
* Scott has plan for using himself and Wayne to set-up a Dwarf Gateway in early December when Wayne returns from India.

h3. DWSM


h6. +Sphere+

* Spheres are finished at Tapemation (YEAH\!\!), and we will ship back to Wah Chang for dye testing.&nbsp; Dye testing =$500 total.&nbsp; Unknown shipping costs.
* Titanium vs. SS sphere fastners.&nbsp; We discussed; TI=$1800, SS = $200 but will need to be replaced.&nbsp; We will buy TI.
* Min-K's to arrive Dec. 15
* As soon as dye tests finished we will schedule a Port Hueneme pressure test.
* Syntactic foam to arrive by Jan 1-2nd.&nbsp; We will need to send foam out for machining.

h6. +DWSM+

* &nbsp;Sample can is ready for valve actuators and motors+pumps.
* Resample can is still waiting mounting parts, but then just needs tubing bends; pumps already mounted
* 1st week of Dec is when we can start running it.
* Doug wants to purchase some extra motors since we have 0 (zero) extra's currently
* Doug will get r-valve boards and actuator mounts from Addie Monday or Tuesday next week.

h3. GUI Development

* &nbsp;Data import now working in the GUI
* Now it is not necessary to parse through the log files .&nbsp; Still some minor bugs to work through, but Kevin will meet with Brent about this.

h3. Other Items:

* &nbsp;  Scott will run next week's meeting in Jim's absence.
* Scott wants to clean GG of all fluid so he can run a \-5C test with EtOH to check the new 'cold' syringes.&nbsp; Scholin to confer with his team about cleaning GG.&nbsp;
* Will need to purchase 12 sets of batteries for elevator (~$40K)
* &nbsp;WE MUST START THINKING ABOUT ORDERING MORE PUCKS for the NEW MACHINES.
* Ship Schedule: currently working of Revision 1.&nbsp; Much discussion about moving Aug6 day to sometime in April.&nbsp; We will finalize this move next week.\\ \\
| (!) | *Remember*\\
 Please remember to use ESD straps in the bldg A lab, as most of its chairs and countertops have failed ESD testing.&nbsp; Dick Littlefield looking into seat\- |]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision
# [25Jun2009]
# 02Jul2009 -- no meeting; 4th of July break
# [09Jul2009]
# [16Jul2009]
# [23Jul2009]
# 30Jul2009 -- Scott ran mtg; proposal preparation
# [06Aug2009]
# 13Aug2009 -- cancelled; proposal/grant preparations
# [20Aug2009]]]></property>
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<property name="body"><![CDATA[# [Comments from July 9, 2008 Design Review]
# [Doug's collected comments of 9 july CDR]

* [The DWSM scheme |DWSM--4k Deep Water Sampling Module^4k DWSM Operation.ppt] (in particular see slide #3)]]></property>
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering member to try to determine what the GUI needs to do.  The following requirements were gathered as part of that process:

h3. Requirements
{section}
{column:width=60%}
||Number||Requirement||Associated View||
|1|User can define missions by specifying phases|Planning|
|2|User can specify and adjust phase start times|Planning|
|3|User can also specify a time to wait between events instead of a specific start time|Planning|
|4|Be able to add non-phase/protocol events (user defined) to the calendar anywhere|Operation|
|5|Be able to set mission start end times that are not associated with a phase/protocol|Planning|
|6|Be able to specify comments associated with missions that are printed at the top of the mission script|Planning|
|7|User shall be able to add comments to a phase that will be generated in the script|Planning|
|8|User shall be able to view images associated with phases|Operation|
|9|User shall be able to browse the .GAL file along with image and filter paper information|Operation|
|10|User should be able to browse image, click on intensity and application applies .GAL/Map with standard curves to give density|Operation|
|11|User should be able to browse the low-res images that come over the telemetry until full size image is offloaded after recovery|Operation|
|12|User should be able to associate external files with events (excel spreadsheet, documents, etc.)|Planning,Operation|
|13| Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power|Operation|
|14|After planning, application should generate mission script, puck loads, and reagent volumes|Planning|
|15|Users should have a form to add/delete/edit protocol runs and phases|Planning|
|16|Users should have a form to add/delete/edit consumables|Planning|
|17|In application users should have sample volume listed with protocol run|Planning|
|18|When users selects a protocol run/phase, the contextual data (CTD/ISUS) should somehow be shown|Operation|
|19|Tide and phase information should be available during planning|Planning,Operation|
|20|Application should allow for details of flushes to be seen/accounted for|Operation|
|21|Users should be able to schedule Kills (end purges) or disable kills|Planning|
|22|Users should be able to define generic events and what script will actually be added to the master script (if needed)|Planning|
|23|Users should be able to download instrument logs and images and the GUI will parse out the following events: 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time|Operation|
|24|Users should be able to visualize the current state of the instrument|Operation,State|
|25|Users should be able to scroll back in time and visualize instrument state at the various points in time|State|
{column}
{column:width=40%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
{panel}
{panel:title=Supporting Docs}
# [Terminology]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
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<property name="body"><![CDATA[h1. Project Pages

h3. GUI Product
# [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
# [JAR file to run locally|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar]
## NOTE: To run this, download the JAR file to a local directory.
## Open a command line (terminal) and change into the directory with the jar file
## Now run: 'java -xvf esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar' which will explode a bunch of files in that directory.
## Now run: 'java -cp .:esp-gui-0.1-SNAPSHOT-jar-with-dependencies.jar org.mbari.esp.gui.ESPPlanner' which will start the application

h3. Bug Tracking:
To report issues with the ESP GUI, please use our bug tracking system, JIRA:
# [Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]

h3. Project Documentation:
# [Requirements (and Gathering)|Requirements (and Gathering) Documentation]
# [Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]

]]></property>
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<property name="body"><![CDATA[In order for McLane to get access to the source code for the ESP, it was deemed that a CVS server in the DMZ with the source code rsync'd out was probably the best option. The machine prey.mbari.org was deemed as the best fit.  In order to configure prey for this work, the following steps were taken:

# Logged in a root
# ran up2date cvs to install the cvs and received the following:
{noformat}
[root@prey home]# up2date cvs

Fetching Obsoletes list for channel: rhel-ia64-es-4...

Fetching rpm headers...
########################################

Name                                    Version              Rel               Arch
----------------------------------------------------------------------------------------
cvs                                     1.11.17             11.el4              ia64  


Testing package set / solving RPM inter-dependencies...
########################################
cvs-1.11.17-11.el4.ia64.rpm ########################## Done.                   
Preparing              ########################################### [100%]

Installing...
   1:cvs                    ########################################### [100%]
[root@prey home]# 
{noformat}
# Created the home directory for cvs
{noformat}
[root@prey home]# mkdir /home/cvs
{noformat}
# I initialized the cvs home directory using
{noformat}
[root@prey cvs]# cvs -d /home/cvs init
{noformat}
This created the CVSROOT directory and populated it with the necessary files.
# I then created the two cvs related groups using
{noformat}
[root@prey cvs]# groupadd cvsusers
[root@prey cvs]# groupadd cvsadmin
{noformat}]]></property>
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<property name="body"><![CDATA[In order for McLane to get access to the source code for the ESP, it was deemed that a CVS server in the DMZ with the source code rsync'd out was probably the best option. The machine prey.mbari.org was deemed as the best fit.  In order to configure prey for this work, the following steps were taken:

# Logged in a root
# ran up2date cvs to install the cvs and received the following:
{noformat}
[root@prey home]# up2date cvs

Fetching Obsoletes list for channel: rhel-ia64-es-4...

Fetching rpm headers...
########################################

Name                                    Version              Rel               Arch
----------------------------------------------------------------------------------------
cvs                                     1.11.17             11.el4              ia64  


Testing package set / solving RPM inter-dependencies...
########################################
cvs-1.11.17-11.el4.ia64.rpm ########################## Done.                   
Preparing              ########################################### [100%]

Installing...
   1:cvs                    ########################################### [100%]
[root@prey home]# 
{noformat}
# Created the home directory for cvs
{noformat}
[root@prey home]# mkdir /home/cvs
{noformat}
# I initialized the cvs home directory using
{noformat}
[root@prey cvs]# cvs -d /home/cvs init
{noformat}
This created the CVSROOT directory and populated it with the necessary files.
# I then created the two cvs related groups using
{noformat}
[root@prey cvs]# groupadd cvsusers
[root@prey cvs]# groupadd cvsadmin
{noformat}
# Created a cvs user (and group) using:
{noformat}
[root@prey cvs]# groupadd cvs
[root@prey cvs]# useradd cvs -g cvs
{noformat}
# Added the CVSROOT environment variable by adding the following to /etc/profile
{noformat}
# Export the CVSROOT directory
CVSROOT=/home/cvs

export CVSROOT
{noformat}
# I set the cvs executable permissions so that it can be run as a service
{noformat}
[root@prey bin]# chmod 2755 /usr/bin/cvs
{noformat}
# Finally, I created the file /etc/xinetd.d/cvs and put the following in that file:
{noformat}
 service cvspserver
 {
         disable            = no
         socket_type    = stream
         wait                = no
         user                = cvs
         group              = cvs
         log_type          = FILE /var/log/cvspserver
         protocol          = tcp
         env                 = '$HOME=/home/cvs'
         bind                = 134.89.2.27
         log_on_failure  += USERID
         port                = 2401
         server             = /usr/bin/cvs
         server_args     = -f --allow-root=/home/cvsroot pserver
 }
{noformat}]]></property>
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<property name="body"><![CDATA[In order for McLane to get access to the source code for the ESP, it was deemed that a CVS server in the DMZ with the source code rsync'd out was probably the best option. The machine prey.mbari.org was deemed as the best fit.  In order to configure prey for this work, the following steps were taken:

1. Logged in a roort
2. ran 'up2date cvs' to install the cvs and received the following:
{noformat}
[root@prey home]# up2date cvs

Fetching Obsoletes list for channel: rhel-ia64-es-4...

Fetching rpm headers...
########################################

Name                                    Version              Rel               Arch
----------------------------------------------------------------------------------------
cvs                                     1.11.17             11.el4              ia64  


Testing package set / solving RPM inter-dependencies...
########################################
cvs-1.11.17-11.el4.ia64.rpm ########################## Done.                   
Preparing              ########################################### [100%]

Installing...
   1:cvs                    ########################################### [100%]
[root@prey home]# 
{noformat}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. &nbsp;


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. &nbsp;


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
 
h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] -- first discussion of adaptive sampling strategies
# Mar 3 -- CMORE Hawaii
# [Mar 10]
# [Mar 17]
# [Mar 24]
# Mar 31 -- team deploying MOE at M0; Brent at WHOI]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Scott, Bill, Kevin, Brent, Chris P, Chris S., Doug, Jim

h3. JdF Preparations

h4. Wand
* Doug's selected a tubing (150F limit and metal reinforced) that looks promising.&nbsp; 30' necessary; may need to heat it to get curl out.
* Pumps and fittings are here.
* Need to check with Pete on whether Ti screen is necessary, or is SS okay?
* Brent leaving June 9 - July 6.&nbsp; Must do much rejiggering
h4. DWSM
* New encoder is in and has depressurized from 3100psi (but did have 900W peak\!)
* Sample bags still has broken switches
* Resample side needs hydraulic damper added
h4. Other
* ISUS.&nbsp; Will check with Luke on where the development of Deep ISUS is.
* ISMS.&nbsp; Must have it before tank testing.
h4. Dates

&nbsp;April 25 \-\- First build of DWSM and wand test.&nbsp; Probes from Pete should be ready for printing.

April 27 \-\- Roman returns from WHOI

May 2 \-\- Core testing begins.&nbsp; Sphere Electronics are in.

May 9 \-\- Second DWSM build

May 16 \-\- Gordon Ready?

May 27 \-\- Gordon must be in ball&nbsp; (this likely to move FORWARD, as we'll be ready sooner)

June 20 \-\- In test tank

h3. Software

* GUI.&nbsp; Would be good to get Stanford folks access to GUI and link shore-station data to our external FTP-site.
* Kevin to look into getting I.S. to r-sync to shore station and deal with this.

h3. WHOI Deployment

* Bruce has made it\!\!
* Reminded that we should try and get acceleration data on our moorings in this area of fast tides.
* Scott got Andy's accelerometers (pieces) and will build two...&nbsp;
* We must still press WHOI to mount CTD on ESP-Chris so we know what's going on down at the can.]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] -- first discussion of adaptive sampling strategies
# Mar 3 -- CMORE Hawaii
# [Mar 10]
# [Mar 17]
# [Mar 24]
# Mar 31 -- team deploying MOE at M0; Brent at WHOI
# [Apr 7]]]></property>
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<property name="body"><![CDATA[h2. For the developers

# [Getting the source|http://kahuna.shore.mbari.org/viewvc/esp/trunk/]
# [Opening in an IDE]
# [Image Processing]]]></property>
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<property name="body"><![CDATA[Still getting up to speed on where I was at.  I used Enterprise Architect to reverse engineer the Java code for the whole GUI part of the project as well as created a nice Data Model from the database on Fog.  VERY NICE!]]></property>
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<property name="body"><![CDATA[h5. Background

In order to really interact with the ESP, it was clear that some level of Ruby integration would really be best in the GUI.  For this reason, I turned to JRuby in order to be able to access a Ruby engine from within the GUI.  I used the information here:

http://kenai.com/projects/jruby/pages/RedBridge

to get me going.  I chose the Embed Core way of doing it as I thought it would be the best way to do what we need to do.

h5. The Ruby environment

In order to understand much about the scripts, the Ruby interpreter uses several environment variables to figure out what context and configuration the ESP is running in.  Those variables are:

# *ESPhome* - is the top level (root) directory of the ESP source code tree.  
# *ESPname* - is the name of the ESP machine. Note this may be the hostname of the machine that it is running on, minus any "esp" that is prefix removed.
# *ESPmode* - is the operating mode in which to run the ESP software
# *ESPlog* - is the root directory under which all data files are written
# *ESPpath* - is a list of directory to search for mission scripts
# *ESPconfigPath* - is a list of directories to search for configuration files

In the GUI, it can interface with one or more ESP, so basically, these variables should be stored with the instrument information. The strange thing about this is that they will only be applicable on the machine where the ESP software is running, which may or may not be where the GUI is running.

h5. Interactions

All of the ruby code for interacting with the ESP is located in MBARI's CVS system.  In order to reference the ruby scripts, they need to be in the classpath for JRuby.  I thought the best way was to have the user point to the head of the directory tree and then basically have the GUI crawl that and build the JRuby classpath dynamically.

The ]]></property>
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<property name="body"><![CDATA[h5. Background

In order to really interact with the ESP, it was clear that some level of Ruby integration would really be best in the GUI.  For this reason, I turned to JRuby in order to be able to access a Ruby engine from within the GUI.  I used the information here:

http://kenai.com/projects/jruby/pages/RedBridge

to get me going.  I chose the Embed Core way of doing it as I thought it would be the best way to do what we need to do.

h5. Interactions

All of the ruby code for interacting with the ESP is located in MBARI's CVS system.  In order to reference the ruby scripts, they need to be in the classpath for JRuby.  I thought the best way was to have the user point to the head of the directory tree and then basically have the GUI crawl that and build the JRuby classpath dynamically.]]></property>
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<property name="body"><![CDATA[h5. Background

In order to really interact with the ESP, it was clear that some level of Ruby integration would really be best in the GUI.  For this reason, I turned to JRuby in order to be able to access a Ruby engine from within the GUI.  I used the information here:

http://kenai.com/projects/jruby/pages/RedBridge

to get me going.  I chose the Embed Core way of doing it as I thought it would be the best way to do what we need to do.

h5. Interactions

All of the ruby code for interacting with the ESP is located in MBARI's CVS system.  ]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI. ]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation. Done in three stages
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}


]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:
{section}
{column}
!Logical Deployment Diagram.jpg|thumbnail,align=center!
{column}
{column:width=60%}
{panel:title=Things to note}
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.
{panel}
{column}
{section}


So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

||Mockup||Notes||
|{mockup:Top Level|12}|A mockup of what the user might see upon first starting the application.|
|{mockup:InstrumentSelect|3}|Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?
Here is the mockup showing what might happen if the user selected one of the instruments.|
|{mockup:DeploymentSelect|3}|After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times|
|{mockup:MouseOverEvent|2}\\{mockup:EventDetails|2}|In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open.|




There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Data Import

{mockup:Data_Import|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



]]></property>
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<property name="body"><![CDATA[h5. Background

In order to really interact with the ESP, it was clear that some level of Ruby integration would really be best in the GUI.  For this reason, I turned to JRuby in order to be able to access a Ruby engine from within the GUI.  I used the information here:

http://kenai.com/projects/jruby/pages/RedBridge

to get me going.  I chose the Embed Core way of doing it as I thought it would be the best way to do what we need to do.

h5. The Ruby environment

In order to understand much about the scripts, the Ruby interpreter uses several environment variables to figure out what context and configuration the ESP is running in.  Those variables are:

# *ESPhome* - is the top level (root) directory of the ESP source code tree.  
# *ESPname* - is the name of the ESP machine. Note this may be the hostname of the machine that it is running on, minus any "esp" that is prefix removed.
# *ESPmode* - is the operating mode in which to run the ESP software
# *ESPlog* - is the root directory under which all data files are written
# *ESPpath* - is a list of directory to search for mission scripts
# *ESPconfigPath* - is a list of directories to search for configuration files

In the GUI, it can interface with one or more ESP, so basically, these variables should be stored with the instrument information. The strange thing about this is that they will only be applicable on the machine where the ESP software is running, which is NOT where the GUI will be running.  The reason to have this information in the GUI however is that at some point the GUI will have to get access to the same source code tree and so even though the ESPhome and ESPlog variables will be different, everything else will be relative to those root directories.  Here is a logical deployment of the ESP network and a GUI client.

{gliffy:name=GUI ESP Deployment|space=ESPAPP|page=Ruby integration|pageid=11239895|align=left|size=L}

h5. Interactions

All of the ruby code for interacting with the ESP is located in MBARI's CVS system.  In order to reference the ruby scripts, they need to be in the classpath for JRuby.  I thought the best way was to have the user point to the head of the directory tree and then basically have the GUI crawl that and build the JRuby classpath dynamically.

The scripts that were active during the ESP's run will be co-located on the FTP server where the logs and images are stored.]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074' N, 70' 36.828"W.&nbsp; Depth 5-9m.]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] -- first discussion of adaptive sampling strategies
# Mar 3 -- CMORE Hawaii
# [Mar 10]
# [Mar 17]
# [Mar 24]
# Mar 31 -- team deploying MOE at M0; Brent at WHOI
# [Apr 7]
# [Apr 14]]]></property>
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<property name="body"><![CDATA[h5. Background

In order to really interact with the ESP, it was clear that some level of Ruby integration would really be best in the GUI.  For this reason, I turned to JRuby in order to be able to access a Ruby engine from within the GUI.  I used the information here:

http://kenai.com/projects/jruby/pages/RedBridge

to get me going.  I chose the Embed Core way of doing it as I thought it would be the best way to do what we need to do.

h5. The Ruby environment

In order to understand much about the scripts, the Ruby interpreter uses several environment variables to figure out what context and configuration the ESP is running in.  Those variables are:

# *ESPhome* - is the top level (root) directory of the ESP source code tree.  
# *ESPname* - is the name of the ESP machine. Note this may be the hostname of the machine that it is running on, minus any "esp" that is prefix removed.
# *ESPmode* - is the operating mode in which to run the ESP software
# *ESPlog* - is the root directory under which all data files are written
# *ESPpath* - is a list of directory to search for mission scripts
# *ESPconfigPath* - is a list of directories to search for configuration files

In the GUI, it can interface with one or more ESP, so basically, these variables should be stored with the instrument information. The strange thing about this is that they will only be applicable on the machine where the ESP software is running, which is NOT where the GUI will be running.  The reason to have this information in the GUI however is that at some point the GUI will have to get access to the same source code tree and so even though the ESPhome and ESPlog variables will be different, everything else will be relative to those root directories.  Here is a logical deployment of the ESP network and a GUI client.

{gliffy:name=GUI ESP Deployment|space=ESPAPP|page=Ruby integration|pageid=11239895|align=left|size=L}

h5. Interactions

All of the ruby code for interacting with the ESP is located in MBARI's CVS system.  In order to reference the ruby scripts, they need to be in the classpath for JRuby.  I thought the best way was to have the user point to the head of the directory tree and then basically have the GUI crawl that and build the JRuby classpath dynamically.

The ]]></property>
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<property name="body"><![CDATA[{gliffy:name=GUI ESP Deployment|space=ESPAPP|page=Ruby integration|pageid=11239895|align=left|size=L}
h5. Background

In order to really interact with the ESP, it was clear that some level of Ruby integration would really be best in the GUI.  For this reason, I turned to JRuby in order to be able to access a Ruby engine from within the GUI.  I used the information here:

http://kenai.com/projects/jruby/pages/RedBridge

to get me going.  I chose the Embed Core way of doing it as I thought it would be the best way to do what we need to do.

h5. The Ruby environment

In order to understand much about the scripts, the Ruby interpreter uses several environment variables to figure out what context and configuration the ESP is running in.  Those variables are:

# *ESPhome* - is the top level (root) directory of the ESP source code tree.  
# *ESPname* - is the name of the ESP machine. Note this may be the hostname of the machine that it is running on, minus any "esp" that is prefix removed.
# *ESPmode* - is the operating mode in which to run the ESP software
# *ESPlog* - is the root directory under which all data files are written
# *ESPpath* - is a list of directory to search for mission scripts
# *ESPconfigPath* - is a list of directories to search for configuration files

In the GUI, it can interface with one or more ESP, so basically, these variables should be stored with the instrument information. The strange thing about this is that they will only be applicable on the machine where the ESP software is running, which may or may not be where the GUI is running.

h5. Interactions

All of the ruby code for interacting with the ESP is located in MBARI's CVS system.  In order to reference the ruby scripts, they need to be in the classpath for JRuby.  I thought the best way was to have the user point to the head of the directory tree and then basically have the GUI crawl that and build the JRuby classpath dynamically.

The ]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Bill, Brent, Jim, Doug

h3. Discussion Items:

* Airflow sciences has been given the PO to perform calculations on a 10.5' vehicle.&nbsp; They are working on it now.&nbsp; Results in \~1 week (?).
* Note sent to Tong Chen of Teledyne describing high-level needs for sampler component to see if they might be interested in collaborating.&nbsp; He forwarded to Mike Metcalf and 'others'.

h4. DWSM

* Doug testing a new bag cap assembly.&nbsp; This led to a lengthy tutorial on the construction of the bag cap and the problems he's seeing with the pressure compensation component.&nbsp; Now we know what the problem is (too much oil in the compensation-side of the system), such that the bag-empty switch is not thrown.&nbsp; Switches always seem fine; it's the hydraulic line that is&nbsp; leaking.&nbsp; Unclear why/how this leakage is occurring.
* Still on track for a first build of DWSM on Monday, April 25.
* Doug has wand designed; parts going into shop soon.&nbsp; Will work with Scott to have complete electrical build of the wand system finished next week for testing.

h4.


h4. ESP Drifter

* Brent has been wrestling with his choice of host board.&nbsp; Finally can write files to internal flash, but must turn off lots of bells and whistles, making board much slower.&nbsp; Now will start layering things onto this board.&nbsp;
* Moxa boards work with the x86 but unclear if it works on embedded host.&nbsp; This is next hurdle.
* Will meet with Gene and Doug Monday to discuss Gene's battery tube needs.&nbsp; Might be some issues with the size he needs.]]></property>
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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# [Extracting the intensities values from the filter image (_Data Extraction_)|#data]

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}

h1. {anchor:data}Data Extraction

Without being able to align the filter image with the GAL points, it's impossible to:
# Associate a spot with it's content
# Accurately and reliable extract all spots of interest.

Here's a few examples of just trying to extract spots from an image:
{info:title=The Good}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_3-40s.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1.tif.png!
{info}
{info:title=The Bad}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-40s.tif.png!
{info}
{info:title=The Ugly}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}

h1. Summary

The only hurdle that needs to be overcome at this point is [pattern matching/image registration|#matching]

Here are the signficant hurdles for _pattern matching/image regsitration_:
# Reliably extracting spots from the filter image
#* In my test images, I was only able to extract all spots in one image using thresholding techniques.
#* Another technique to try would be edge detection. This may be problematic in noisier images though. 
# Dealing with symmetry in the spot layout, this confounds most image registration techniques.
#* It would be great if I could get some *key spots* that I can reliably detect and differentiate from the other spots. For example, 2 spots that are near the edge of the disk. If I could extract those then, I would be able to easily register the GAL file with the image. As an example, look at the image above an notice the single spot near the edge of the disk. If we had 2 of those on that image it would make my life much simpler!! ;-) ALthough in order to use those I would need be able to extract the same 2 spots from the GAL file.

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<property name="body"><![CDATA[{gliffy:name=wand plumping|space=ESPAPP|page=Apr 21|pageid=16777299|align=left|size=L}
Present:&nbsp; Bill, Brent, Jim, Doug

h3. Discussion Items:

* Airflow sciences has been given the PO to perform calculations on a 10.5' vehicle.&nbsp; They are working on it now.&nbsp; Results in \~1 week (?).
* Note sent to Tong Chen of Teledyne describing high-level needs for sampler component to see if they might be interested in collaborating.&nbsp; He forwarded to Mike Metcalf and 'others'.

h4. DWSM

* Doug testing a new bag cap assembly.&nbsp; This led to a lengthy tutorial on the construction of the bag cap and the problems he's seeing with the pressure compensation component.&nbsp; Now we know what the problem is (too much oil in the compensation-side of the system), such that the bag-empty switch is not thrown.&nbsp; Switches always seem fine; it's the hydraulic line that is&nbsp; leaking.&nbsp; Unclear why/how this leakage is occurring.
* Still on track for a first build of DWSM on Monday, April 25.
* Doug has wand designed; parts going into shop soon.&nbsp; Will work with Scott to have complete electrical build of the wand system finished next week for testing.

h4.


h4. ESP Drifter

* Brent has been wrestling with his choice of host board.&nbsp; Finally can write files to internal flash, but must turn off lots of bells and whistles, making board much slower.&nbsp; Now will start layering things onto this board.&nbsp;
* Moxa boards work with the x86 but unclear if it works on embedded host.&nbsp; This is next hurdle.
* Will meet with Gene and Doug Monday to discuss Gene's battery tube needs.&nbsp; Might be some issues with the size he needs.]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] -- first discussion of adaptive sampling strategies
# Mar 3 -- CMORE Hawaii
# [Mar 10]
# [Mar 17]
# [Mar 24]
# Mar 31 -- team deploying MOE at M0; Brent at WHOI
# [Apr 7]
# [Apr 14]
# [Apr 21]]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument and the various places it will live.  That diagram is shown here:
{section}
{column}
{gliffy:name=ESP Data Overview|space=ESPAPP|page=Design|pageid=6258757|align=left|size=M}
{column}
{column:width=60%}
{panel:title=Things to note}
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station (this includes the ruby scripts used to run the ESP).
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.
{panel}
{column}
{section}


So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

||Mockup||Notes||
|{mockup:Top Level|12}|A mockup of what the user might see upon first starting the application.|
|{mockup:InstrumentSelect|3}|Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?
Here is the mockup showing what might happen if the user selected one of the instruments.|
|{mockup:DeploymentSelect|3}|After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times|
|{mockup:MouseOverEvent|2}\\{mockup:EventDetails|2}|In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open.|




There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Data Import

{mockup:Data_Import|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]
# [Apr 12] \-\- Roman at WHOI, Chris P Europe]]></property>
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<property name="body"><![CDATA[As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument and the various places it will live.  That diagram is shown here:
{section}
{column}
{gliffy:name=ESP Data Overview|space=ESPAPP|page=Design|pageid=6258757|align=left|size=M}
{column}
{column:width=60%}
{panel:title=Things to note}
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.
{panel}
{column}
{section}


So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

||Mockup||Notes||
|{mockup:Top Level|12}|A mockup of what the user might see upon first starting the application.|
|{mockup:InstrumentSelect|3}|Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?
Here is the mockup showing what might happen if the user selected one of the instruments.|
|{mockup:DeploymentSelect|3}|After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times|
|{mockup:MouseOverEvent|2}\\{mockup:EventDetails|2}|In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open.|




There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Data Import

{mockup:Data_Import|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]
# [Apr 12] \-\- Roman at WHOI, Chris P Europe
# Apr 19
# Apr 26]]></property>
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<property name="body"><![CDATA[{gliffy:name=ESP Data Overview|space=ESPAPP|page=Design|pageid=6258757|align=left|size=M}
As a first step in designing the application to act as the Graphical User Interface (GUI) for the ESP instrument(s), a diagram was created to capture the existing structure of the digital information that will need to be tracked for each ESP instrument.  That diagram is shown here:
{section}
{column}
!Logical Deployment Diagram.jpg|thumbnail,align=center!
{column}
{column:width=60%}
{panel:title=Things to note}
# The ESP instrument creates and appends content to some directory on the main CPU.
# An FTP server makes that content available to the outside world.
# The shore station takes the FTP content from the deployed ESP and creates a mirror of the content on the shore station.
# On the shore station, it can be managing content from more than one ESP and by a manual convention, old deployments are named YYMMM.espname.
# The .log files are files that have to be read in by a Ruby application as they are serialized Ruby objects and so need Ruby to interpret them
# The ESP process is basically started with a 'nohup' command and any console messages are then routed to the .out file.
# The link is not always strong over the Freewave so communication can sometimes be very slow.
# If a command GUI wishes to send commands directly to the ruby interpreter running on the ESP itself, a slow link would cause major issues.
# The data is then manually copied to the \\tornado\esp directory under a different layout than that of the shore station. The list below shows the directory structure on
\\
tornado which means that the 'esp' directory on tornado may actually be the YYMMM.espname directory on the shore station.
## YYMMM
### espname
#### esp
# The 'messages' file is simply a symbolic link to the /var/messages so that the FTP mirror will pick them up for debugging.
{panel}
{column}
{section}


So, in order to manage the data through some application, it is good to realize that the data will mostly have three locations through time:
# The ESP instrument itself.  This data is created during the deployment, is transmitted back to shore but is NOT kept permanently on the ESP instrument itself.
# The shore station. This is an FTP synch of the data on the ESP itself and, assuming connectivity is there, will be a duplicate copy of what is deployed on the ESP itself.  This will outlive the data stored on the instrument itself, but it's parent directory may be renamed when a new deployment comes up.
# 'Permanent' storage location.  This is a copy of the data that will be stored somewhere that will be a final resting place for all intents and purposes.  There is a directory structure that will be adhered to and should provide a common location for all the data from the ESPs.  This is sort of a post-deployment activity and should not be relied upon for storage during the deployment.

Next, the design group sat down to create a model that would allow the application to capture all the concepts that need to be managed in the GUI application.  That data model is available at the link below.
# [Data Model]

Once this model was developed to capture the concepts that will need to be stored persistently, we went to work on some mockups of what the GUI might look like. From an end user's point of view, the application will basically serve two needs: Operation of the instrument(s) and analysis of the data from the instrument(s).  To meet the requirements, various GUI components will be needed (terms are from data model):
# Create Instrument
# Edit Instrument
# Delete Instrument
# Create ProtocolType
# Edit ProtocolType
# Delete ProtocolType
# Create PhaseType
# Edit PhaseType
# Delete PhaseType
# Add ProtocolTypes to PhaseTypes
# Remove ProtocolTypes from PhaseTypes
# Create ConsumableType
# Edit ConsumableType
# Delete ConsumableType
# Create/Add a ConsumableAmount by creating a connection between ProtocolType and ConsumableType using an amount to characterize the link.
# Edit the ConsumableAmount link
# Delete a ConsumableAmount from a ProtocolType
# Create EventType (Default events should be DEPLOYMENT, PHASE, PROTOCOL_RUN)
# Edit EventType
# Delete EventType
# Create Deployment for Instrument
# Edit Deployment
# Delete Deployment (This will cascade delete events attached to it)
# Create Bag
# Edit Bag
# Delete Bag
# Add Bag to Deployment (for reagents, waste and power)
# Create and Add a Phase (instance of PhaseType) to Deployment
# Edit Phase
# Delete Phase (and all child events)
# Create Resource (HTTP accessible content)
# Attach Resource to Deployment or Phase
# Delete Resource (not the Resource itself, just the information about it).
# Create an Image (HTTP accessible image)
# Attach Image to Deployment or Phase
# Delete Image (not the actual image, just the information about it).
# View the Tide web service and add the specific location to the list of interesting locations
# Remove tide location
# Create new Comment
# Attach comment to any event, image, or resource
# Delete comment

h5. Log file interface

In order to get this information from the ESP system, the GUI needs and interface to the ESP which ended up being the log file.  The documentation for that interface can be found at [ESP Log Interface]

h5. Mockups

Now, if we think about sitting down at the GUI and starting it up, I would think the first view we would want is sort of an operational view of things.  The things I would like to see are:
# ESPs available
# Overall calendar showing all planned deployments and logged events for past and current deployments. (should be able to flip this on/off quickly when I want to dive into one instrument).

||Mockup||Notes||
|{mockup:Top Level|12}|A mockup of what the user might see upon first starting the application.|
|{mockup:InstrumentSelect|3}|Logically, the next step would be for the user to explore the information presented:
# Information about each ESP
## Serial Number
## Picture?
Here is the mockup showing what might happen if the user selected one of the instruments.|
|{mockup:DeploymentSelect|3}|After learning about the instrument, I might want to know more about the deployments (past, present and future). The user could then select a deployment from a list or on the calendar and find the following information:
# Name, geospatial location
# List of scheduled phases with start times|
|{mockup:MouseOverEvent|2}\\{mockup:EventDetails|2}|In this view, the individual events (including phases would show up on the calendar and the user could then mouse over events to get more details.  These events would include comments, logged events, etc. If the user then clicks on an event in either the calendar or in the list of scheduled phases, a dialog box with more details would open.|




There will also be a tab to let the user see a table list of all events for the selected deployment (both scheduled and actual).  The same dialog box will show if the events are double clicked in the event list.

{mockup:DeploymentPlannedResources|2}

{mockup:ConsumedResources|2}

h5. Instrument Dialog Box

{mockup:InstrumentDialog|1}

h5. Deployment Dialog

{mockup:DeploymentDialog|1}

h5. Menus
{mockup:ESP_Menu|1}

{mockup:Edit_Menu|1}

h5. Define/Edit Phases and Protocol Templates

{mockup:Phase_Type_Dialog|4}

{mockup:Protocol_Type_Dialog|1}

h5. Data Import

{mockup:Data_Import|1}

h5. Instrument State Visualization

To examine the state of the instrument for various deployments, the user would then select View->Instrument State from the pull down menu.  This would put the user into a new view that shows the instrument state for the selected deployment.  At the bottom is a timeline slider the user can control to change what point in time the state is to be visualized.  There are also play controls to let the user control a playback of instrument states from the past

{mockup:InstrumentStateSelect|2}

{mockup:InstrumentState|1}



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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# [Extracting the intensities values from the filter image (_Data Extraction_)|#data]

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}

h1. {anchor:data}Data Extraction

Without being able to align the filter image with the GAL points, it's impossible to:
# Associate a spot with it's content
# Accurately and reliable extract all spots of interest.

Here's a few examples of just trying to extract spots from an image:
{info:title=The Good}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_3-40s.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1.tif.png!
{info}
{info:title=The Bad}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-40s.tif.png!
{info}
{info:title=The Ugly}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}

h1. Summary

The only hurdle that needs to be overcome at this point is [pattern matching/image registration|#matching]

Here are the signficant hurdles for _pattern matching/image regsitration_:
# Reliably extracting spots from the filter image
#* In my test images, I was only able to extract all spots in one image using thresholding techniques.
#* Another technique to try would be edge detection. This may be problematic in noisier images though. 
# Dealing with symmetry in the spot layout, this confounds most image registration techniques.
#* It would be great if I could get some *key spots* that I can reliably detect and differentiate from the other spots. For example, 2 spots that are near the edge of the disk. If I could extract those then, I would be able to easily register the GAL file with the image. As an example, look at the image above an notice the single spot near the edge of the disk. If we had 2 of those on that image it would make my life much simpler!! ;-) ALthough in order to use those I would need be able to extract the same 2 spots from the GAL file.


h1. Applying Fiducial Marks for Image Analysis

If the ESP arrays had distinct fiducial marks it should be possible to locate these marks and use them for scaling and rotation of the GAL to match the array image. Ideally these fiducial's should be either the closest points to the center of mass of the or the farthest points from the center of mass.

h2. Applying Fiducials. 
* During analysis we extract the spots that are visible using a thresholding technique. This give an image like this: 
!fitler_3_aoi_masked.png!
* From this mask we can calculate a center of mass of the image. (The blue dot represents the center of mass) 
!filter_3-center-of-mass.png!
* To easily locate fiducial it would be best if they were either the points nearest the center-of-mass or farthest from it. The red dots in the images below represent notional fiducial points.
** Example of points nearest COM: 
!filter_3_center_fiducial.png!
** Example of points farthest from COM: 
!filter_3-distal_fiducial.png!




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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# [Extracting the intensities values from the filter image (_Data Extraction_)|#data]

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}

h1. {anchor:data}Data Extraction

Without being able to align the filter image with the GAL points, it's impossible to:
# Associate a spot with it's content
# Accurately and reliable extract all spots of interest.

Here's a few examples of just trying to extract spots from an image:
{info:title=The Good}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_3-40s.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1.tif.png!
{info}
{info:title=The Bad}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-40s.tif.png!
{info}
{info:title=The Ugly}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}

h1. Summary

The only hurdle that needs to be overcome at this point is [pattern matching/image registration|#matching]

Here are the signficant hurdles for _pattern matching/image regsitration_:
# Reliably extracting spots from the filter image
#* In my test images, I was only able to extract all spots in one image using thresholding techniques.
#* Another technique to try would be edge detection. This may be problematic in noisier images though. 
# Dealing with symmetry in the spot layout, this confounds most image registration techniques.
#* It would be great if I could get some *key spots* that I can reliably detect and differentiate from the other spots. For example, 2 spots that are near the edge of the disk. If I could extract those then, I would be able to easily register the GAL file with the image. As an example, look at the image above an notice the single spot near the edge of the disk. If we had 2 of those on that image it would make my life much simpler!! ;-) ALthough in order to use those I would need be able to extract the same 2 spots from the GAL file.


h1. Applying Fiducial Marks for Image Analysis

If the ESP arrays had distinct fiducial marks it should be possible to locate these marks and use them for scaling and rotation of the GAL to match the array image. Ideally these fiducial's should be either the closest points to the center of mass of the or the farthest points from the center of mass.

h2. Applying Fiducials. 
# During analysis we extract the spots that are visible using a thresholding technique. This give an image like this: !fitler_3_aoi_masked.png!
# From this mask we can calculate a center of mass of the image. (The blue dot represents the center of mass) !filter_3_center-of-mass.png!
# To easily locate fiducial it would be best if they were either the points nearest the center-of-mass or farthest from it. The red dots in the images below represent notional fiducial points.
#* Example of points nearest COM: !filter_3_center_fiducial.png!
#* Example of points farthest from COM: !filter_3_distal_fiducial.png!




]]></property>
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</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">11272670</id>
<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# [Extracting the intensities values from the filter image (_Data Extraction_)|#data]

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}

h1. {anchor:data}Data Extraction

Without being able to align the filter image with the GAL points, it's impossible to:
# Associate a spot with it's content
# Accurately and reliable extract all spots of interest.

Here's a few examples of just trying to extract spots from an image:
{info:title=The Good}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_3-40s.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1.tif.png!
{info}
{info:title=The Bad}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-40s.tif.png!
{info}
{info:title=The Ugly}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}

h1. Summary

The only hurdle that needs to be overcome at this point is [pattern matching/image registration|#matching]

Here are the signficant hurdles for _pattern matching/image regsitration_:
# Reliably extracting spots from the filter image
#* In my test images, I was only able to extract all spots in one image using thresholding techniques.
#* Another technique to try would be edge detection. This may be problematic in noisier images though. 
# Dealing with symmetry in the spot layout, this confounds most image registration techniques.
#* It would be great if I could get some *key spots* that I can reliably detect and differentiate from the other spots. For example, 2 spots that are near the edge of the disk. If I could extract those then, I would be able to easily register the GAL file with the image. As an example, look at the image above an notice the single spot near the edge of the disk. If we had 2 of those on that image it would make my life much simpler!! ;-) ALthough in order to use those I would need be able to extract the same 2 spots from the GAL file.


h1. Applying Fiducial Marks for Image Analysis

If the ESP arrays had distinct fiducial marks it should be possible to locate these marks and use them for scaling and rotation of the GAL to match the array image. Ideally these fiducial's should be either the closest points to the center of mass of the or the farthest points from the center of mass.

h2. Applying Fiducials. 
# During analysis we extract the spots that are visible using a thresholding technique. This give an image like this: !fitler_3_aoi_masked.png!
# From this mask we can calculate a center of mass of the image. (The blue dot represents the center of mass) !fitler_3_center-of-mass.png!
# To easily locate fiducial it would be best if they were either the points nearest the center-of-mass or farthest from it. The red dots in the images below represent notional fiducial points.
#* Example of points nearest COM: !filter_3_center_fiducial.png!
#* Example of points farthest from COM: !filter_3_distal_fiducial.png!




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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">11272669</id>
<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# [Extracting the intensities values from the filter image (_Data Extraction_)|#data]

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}

h1. {anchor:data}Data Extraction

Without being able to align the filter image with the GAL points, it's impossible to:
# Associate a spot with it's content
# Accurately and reliable extract all spots of interest.

Here's a few examples of just trying to extract spots from an image:
{info:title=The Good}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_3-40s.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1.tif.png!
{info}
{info:title=The Bad}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-40s.tif.png!
{info}
{info:title=The Ugly}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}

h1. Summary

The only hurdle that needs to be overcome at this point is [pattern matching/image registration|#matching]

Here are the signficant hurdles for _pattern matching/image regsitration_:
# Reliably extracting spots from the filter image
#* In my test images, I was only able to extract all spots in one image using thresholding techniques.
#* Another technique to try would be edge detection. This may be problematic in noisier images though. 
# Dealing with symmetry in the spot layout, this confounds most image registration techniques.
#* It would be great if I could get some *key spots* that I can reliably detect and differentiate from the other spots. For example, 2 spots that are near the edge of the disk. If I could extract those then, I would be able to easily register the GAL file with the image. As an example, look at the image above an notice the single spot near the edge of the disk. If we had 2 of those on that image it would make my life much simpler!! ;-) ALthough in order to use those I would need be able to extract the same 2 spots from the GAL file.


h1. Applying Fiducial Marks for Image Analysis

If the ESP arrays had distinct fiducial marks it should be possible to locate these marks and use them for scaling and rotation of the GAL to match the array image. Ideally these fiducial's should be either the closest points to the center of mass of the or the farthest points from the center of mass.

h2. Applying Fiducials. 
# During analysis we extract the spots that are visible using a thresholding technique. This give an image like this: !fitler_3_aoi_masked.png!
# From this mask we can calculate a center of mass of the image. (The blue dot represents the center of mass) !fitler_3_center-of-mass.png!
# To easily locate fiducial it would be best if they were either the points nearest the center-of-mass or farthest from it.
#* Example of points nearest COM: !filter_3_center_fiducial.png!
#* Example of points farthest from COM: !filter_3_distal_fiducial!




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<property name="body"><![CDATA[h1. Steps Required for Automated Image Analysis
# [Identifying spots on the filter image (_Spot Segmentation_)|#segmentation]
# [Extracting a single filter from the GAL file (_GAL Extraction_)|#extraction]
# [Aligning the GAL spots with the filter spots (Pattern Matching)|#matching]
# [Extracting the intensities values from the filter image (_Data Extraction_)|#data]

{info:title=Image Coordinate Systems}
For this work, all data is referenced using the _image coordinate system_. The upper left corner of an image is the origin (e.g. 0,0). +X is right, +Y is down.
{info}

h2. Example Image

For this document I will be using this image as my filter sample:
!filter_3.png!

h1. {anchor:segmentation}Spot Segmentation

In order to identify the spots on the filter image I tried the following:
h2.  Remove areas outside the filter boundaries from the filter analysis.
* This was determined by using a acceptance radius = (ImageHeight / 2) * 0.25. Pixels out side this radius are ignored
* This is important since the edge of the disk creates high intensity artifacts in the filter image.
!fitler_3_aoi.png!
{code}ImageIOService io = new org.mbari.esp.imaging.services.impl.ImageIOServiceImpl();
ImagePlus ip = io.read((new File('filter_3.tif').toURI().toURL()));
(new org.mbari.esp.imaging.RemoveNonFilterAreaOperation(ip.getProcessor())).run();
io.write(new File('filter_3_roi.png'));
{code}

h2. Apply a thresholding technique to locate spots. 
* From testing a variety of thresholding techiques, the _maximum entropy threshold_ provided the most reliable spot resolution. 
!fitler_3_aoi_masked.png!
{code} ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
ImagePlus mask = gaas.mask(ip);
io.write(new File('filter_3_roi_masked.png'));
{code}
{info:title=Resolving Spots Issue #1: Spot Size} Spots are expected to be rounghly uniform size. To remove outlier spots I run statistics on the spots sizes that appear in the mask and use 90% confidence interval. Spots with sizes out side this range are rejected unless they're size is within a few pixels of a spot that was within the acceptable range. For example, given a set of spot sizes of (20, 12, 11, 10, 9, 8) with accepted spots of (12, 11, 10, 9), 8 would be accepted since it's close to 9 but 20 would not.{info}
{info:title=Resolving Spots Issue #2: Spots Blurring Together}In areas of bright spots grouped togther, it can be difficult to separate individual spots as they blur together when masked. I tried a technique of dilating spots (actually makes the spots smaller) to resolve individual bright spots. Notice in the masked image above that some spots that are discernible to the eye were removed by the code because they blurred together, resulting in a spot with a size that's outside the confidence limits{info}
{info:title=Resolving Spots Issue #3: Bright Image}
There are problems with the thresholding technique when the image is saturated. The image below illustrate the misidentification of spots; red dots indicate where the spots were detected.
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1-160s.tif.jpg!{info}
{info:title=Resolving Spots Issue #4: Bright 'Noise'}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!{info}

h2. Extracting Spot Locations
Once a mask has been created it's relatively easy to 'extract' the spot location. For my analysis, I searched each spot, as defined by the mask, for the brightest 3x3 pixel block within the spot and used that as the spot location. This is useful for attempting to apply point-matching algorithms.
!PointUtilitiesTest-testPlot01.png!
{code:java}ImagePlus ip; // see above code for generating ROI image
GeneArrayAnalysisService gaas = new org.mbari.esp.imaging.services.impl.GeneArrayAnalysisServiceImpl01();
/*
 * Key = unique, but arbitrary, spot ID 
 * Value = x,y location of upper left corner of mean block. z is mean intensity of 3x3 block
 */
Map<Integer, Point3D<Double>> pointMap = gaas.extractIntensities(ip, 3);{code}

h1. {anchor:extraction}GAL Feature Extraction

h2. About GAL Files

Gene-array Layout Files (GAL) define the spots to be printed onto the filter by a piezzo-electric printer. A single GAL file defines multiple filters.
{info:title=ESP GAL files aren't real GALs!}Our printer uses a custom file format. So, while we call them GAL's, since they serve that role, they aren't real GAL files{info}
!ArrayToColorGridTest01-20090504105215-A1-small.png!
{code}GeneArrayIOService io = new org.mbari.esp.imaging.services.impl.GeneArrayIOServiceImpl();
List<GALPoint> points = io.read((new File('my_gal.txt')).toURI().toURL());
BufferedImage image = PiezzoArrayUtil.arrayToColorGrid(points, true, 100);
ImageIO.write(image, "png", new File("my_gal.png"));{code}

h2. Isolating a Single Filter from the GAL points

With a little _apriori_ knowledge, this is pretty simple. Since there is a relatively large spacing between filters, I just create a spot defining the upper left corner (e.g. minimum x and y value of all points), define a box of a certain size (in our case I'm using 12500 units) and remove everything outside the box.
!FilterSingleArrayTest02-20090504105215-GRID.png!
{code}
List<GALPoint> allFilters = io.read((new File('my_gal.txt')).toURI().toURL());
List<GALPoint> oneFilter = PiezzoUtilities.filterSingleSpot(allFilters, 12500);
{code}

h1. {anchor:matching}Pattern Matching

At this point we have 3 important things:
# The original filter image
# Location of a number of spots from the image
# Location of spots for a single filter as defined in the GAL file.
!PointUtilitiesTest-testPlot02.png!

There are a number of techniques for pattern matching. A few that I've explored are described below:

h2. Log-polar transformation.

h3. References
[^Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.pdf]

h3. Evaluation
At first brush, this seems the ideal technique for image registration. It handles rigid transformations involving scaling, rotation, and translation. In order to use this technique I generated an _ideal image_ of the GAL points and attempted to align that with the filter image. For the test image, I was able modify the transform to accuratly align rotation and give relatively good translation. However I was never able to get the image to scale correctly. This is in part due to the similarity of the patterns used in the image. The log-polar transform would create a peak correlation on the wrong patterns between the image. It should also be noted that other test images produced widely varying results. So I do not consider the technique reliable, although with more time, it may be possible to improve upon it.

{info:title=Initial Images}!ImageRegistrationTest01-test01-bestR2.png! !ImageRegistrationTest01-I.png!{info}

{info:title=Log-polar Transform of Images}!ImageRegistrationTest01-test01-bestR2p.png! !ImageRegistrationTest01-Ip.png!
*NOTE* The GAL points image was duplicated vertically to allow account for wrapping of rotation when the cross-correlation is performed{info}

h2. Fourier-Mellin Transform

This is essentially a log-polar transform in Fourier space. I did not have time to pursue it.

h2. Robust Point Set Registration Using Mixture of Gaussians

h3. References
[http://code.google.com/p/gmmreg/]

h3. Evaluation
This is a point set registration technique, so instead of attempting to align images, we are trying to match to different sets of points. This technique allows for both rigid and non-rigid point-set registration, although, in our case, we are only interested in rigid registration. (Non-rigid registration warps the points to fit, which we do not want) I ran the open-source code on our data samples and did not have any luck. I also passed the data on to the author, Bing Jian of this technique. He also was not succesful with the registration. His comments were:
{quote}I took a look at the results and noticed the rigid registration result is not as good as the nonrigid one. Maybe it is because of the scaling issue.{quote}
{quote}Have you found any better solution yet? I think the symmetry presented in the data can cause the local minimum problem.  Do you have any ground truth for this case? I guess I need to add a similarity transform to handle this case.  BTW,  I suggest using the point set with less points as model set for the gmmreg program, but it should not matter too much as both point sets are small.{quote}

h1. {anchor:data}Data Extraction

Without being able to align the filter image with the GAL points, it's impossible to:
# Associate a spot with it's content
# Accurately and reliable extract all spots of interest.

Here's a few examples of just trying to extract spots from an image:
{info:title=The Good}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_3-40s.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_1.tif.png!
{info}
{info:title=The Bad}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2.tif.png!

!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-40s.tif.png!
{info}
{info:title=The Ugly}
!GeneArrayAnalysisServiceImplTest-_imaging_test01_filter_2-160s.tif.jpg!
{info}

h1. Summary

The only hurdle that needs to be overcome at this point is [pattern matching/image registration|#matching]

Here are the signficant hurdles for _pattern matching/image regsitration_:
# Reliably extracting spots from the filter image
#* In my test images, I was only able to extract all spots in one image using thresholding techniques.
#* Another technique to try would be edge detection. This may be problematic in noisier images though. 
# Dealing with symmetry in the spot layout, this confounds most image registration techniques.
#* It would be great if I could get some *key spots* that I can reliably detect and differentiate from the other spots. For example, 2 spots that are near the edge of the disk. If I could extract those then, I would be able to easily register the GAL file with the image. As an example, look at the image above an notice the single spot near the edge of the disk. If we had 2 of those on that image it would make my life much simpler!! ;-) ALthough in order to use those I would need be able to extract the same 2 spots from the GAL file.


h1. Applying Fiducial Marks for Image Analysis

If the ESP arrays had distinct fiducial marks it should be possible to locate these marks and use them for scaling and rotation of the GAL to match the array image. Ideally these fiducial's should be either the closest points to the center of mass of the or the farthest points from the center of mass..
]]></property>
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<property name="body"><![CDATA[Present: Julie, Chris P., Roman, Bill, Jim, Chris S.
\\
\\

{color:#0033ff}1. &nbsp;PCR paper layout. &nbsp;Chris S. will present outline, fig ideas, holes. &nbsp;Discuss which journal to focus it towards.{color}
* Chris started the layout and many decisions still need to be made about how many machines to include in building standard curves, and which deployments.&nbsp; Discussion ensued.&nbsp;
* She will have Figure ideas next Tuesday.
\\

{color:#0000ff}2. &nbsp;M0 leapfrog deployment. &nbsp;Julie, discuss your plan; what are Chris P's, responsibilities in this?{color}
* We need to use only 1 probe set from beginning to end of deployment. MaryAnn from U. Ga, wanted liquid back but that ain't happening.&nbsp; We are still trying to decide which P/P set to use.
* Moe goes out April 15 on Zephyr
* 30 days later, Neo will be flipped for Moe.
\\

{color:#0000ff}3. &nbsp;Do we need new targets for Nov MARS deployment of D-ESP. &nbsp;If yes, must develop libraries?{color}
* {color:#cc0000}Tabled{color}

{color:#0000ff}4. &nbsp;Progress on '08/'09 paper. (John returns 2-12){color}
* {color:#cc0000}Tabled{color}

{color:#0033ff}5. &nbsp;&nbsp;ASLO practice talks. &nbsp;I've reserved Pacific Forum Friday, Feb 19 10am-12.{color}
* Everyone is happy and excited to get their talks done the week before and practice them.

{color:#0000ff}&nbsp;{color}{color:#0000ff}6.&nbsp; Gordon Results{color}
* &nbsp;{color:#cc0000}Tabled{color}

{color:#0000ff}7.&nbsp; New IPC results{color}?
* We will order 10K rxns from Sandy. (or Melancon if he can deal with large number and has approval to be a reagent reseller from ABI)
\\

{color:#0000ff}8.&nbsp; Pete & Vik groups schedule. And are they taking instruments back??{color}\\
* They arrive Monday (MBARI Holiday) but have Chris P phone number.
* Vik bringing 5 p/p sets and will use MFB #9
* Pete's group will bring 1 Cyber, 1TAQ assay, will use MFB #2
* Reasonable target to ship them their MFB's is March, 2010 (Vik first, then Pete's group)
\\

{color:#0000ff}9.&nbsp; MOE script upgrade after Julies MOCK deployment? Should new IPC be included on the MOCK??{color}
* Cold testing will begin this week with Moe.&nbsp; Engineering is standing by to help Julie can the instrument.
* Julie will upgrade scripts after the cold test, but before the deployment.
* I don't remember what we decided about including new IPC into the mock deployment

{color:#0000ff}10.{color}{color:#0000ff}&nbsp;{color} {color:#0000ff}DA testing{color}
* We will begin Bruce DA testing next so Roman can watch it.&nbsp; He's working with Bruce K. now and training is going slowly because there is so much to learn.&nbsp; We will be sending Roman out to WHOI to help with acceptance testing.

{color:#0000ff}11.{color}{color:#0000ff}&nbsp;{color} {color:#0000ff}S. California deployment{color}
* Chris S. working on boat issues, looking like we may use Shanna Rae, but haven't heard from Christmann.&nbsp; S. Cal will put two moorings in San Pedro Bay and run Hab/DA/WCR.&nbsp;
* We need to simply set a date and go there, as the guys down south don't know what to tell us on dates.

Various
* We need to begin a list of how to test extraction and archiving protocols that would work the best.&nbsp; This will get more complicated as other&nbsp; groups start adopting our work.]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]]]></property>
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Present: Julie, Chris P., Roman, Bill, Jim, Chris S.\\ \\

{color:#0033ff}1. &nbsp;PCR paper layout. &nbsp;Chris S. will present outline, fig ideas, holes. &nbsp;Discuss which journal to focus it towards.{color}
* Chris started the layout and many decisions still need to be made about how many machines to include in building standard curves, and which deployments.&nbsp; Discussion ensued.&nbsp;
* She will have Figure ideas next Tuesday. \\

{color:#0000ff}2. &nbsp;M0 leapfrog deployment. &nbsp;Julie, discuss your plan; what are Chris P's, responsibilities in this?{color}
* We need to use only 1 probe set from beginning to end of deployment. MaryAnn from U. Ga, wanted liquid back but that ain't happening.&nbsp; We are still trying to decide which P/P set to use.
* Moe goes out April 15 on Zephyr
* 30 days later, Neo will be flipped for Moe. \\

{color:#0000ff}3. &nbsp;Do we need new targets for Nov MARS deployment of D-ESP. &nbsp;If yes, must develop libraries?{color}
*  {color:#cc0000}Tabled{color}

{color:#0000ff}4. &nbsp;Progress on '08/'09 paper. (John returns 2-12){color}
*  {color:#cc0000}Tabled{color}

{color:#0033ff}5. &nbsp;&nbsp;ASLO practice talks. &nbsp;I've reserved Pacific Forum Friday, Feb 19 10am-12.{color}
* Everyone is happy and excited to get their talks done the week before and practice them.

{color:#0000ff}&nbsp;{color}{color:#0000ff}6.&nbsp; Gordon Results{color}
* &nbsp;{color:#cc0000}Tabled{color}

{color:#0000ff}7.&nbsp; New IPC results{color}?
* We will order 10K rxns from Sandy. (or Melancon if he can deal with large number and has approval to be a reagent reseller from ABI)\\

{color:#0000ff}8.&nbsp; Pete & Vik groups schedule. And are they taking instruments back??{color}\\
* They arrive Monday (MBARI Holiday) but have Chris P phone number.
* Vik bringing 5 p/p sets and will use MFB #9
* Pete's group will bring 1 Cyber, 1TAQ assay, will use MFB #2
* Reasonable target to ship them their MFB's is March, 2010 (Vik first, then Pete's group) \\

{color:#0000ff}9.&nbsp; MOE script upgrade after Julies MOCK deployment? Should new IPC be included on the MOCK??{color}
* Cold testing will begin this week with Moe.&nbsp; Engineering is standing by to help Julie can the instrument.
* Julie will upgrade scripts after the cold test, but before the deployment.
* I don't remember what we decided about including new IPC into the mock deployment

{color:#0000ff}10.{color}{color:#0000ff}&nbsp;{color} {color:#0000ff}DA testing{color}
* We will begin Bruce DA testing next so Roman can watch it.&nbsp; He's working with Bruce K. now and training is going slowly because there is so much to learn.&nbsp; We will be sending Roman out to WHOI to help with acceptance testing.

{color:#0000ff}11.{color}{color:#0000ff}&nbsp;{color} {color:#0000ff}S. California deployment{color}
* Chris S. working on boat issues, looking like we may use Shanna Rae, but haven't heard from Christmann.&nbsp; S. Cal will put two moorings in San Pedro Bay and run Hab/DA/WCR.&nbsp;
* We need to simply set a date and go there, as the guys down south don't know what to tell us on dates.

Various
* We need to begin a list of how to test extraction and archiving protocols that would work the best.&nbsp; This will get more complicated as other&nbsp; groups start adopting our work. ]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] \- first discussion of adaptive sampling strategies
# Mar 3 - CMORE Hawaii
# [Mar 10] \-\- wand schematic
# [Mar 17]
# [Mar 24]
# Mar 31 - team deploying MOE at M0; Brent at WHOI
# [Apr 7]
# [Apr 14]
# [Apr 21]\--wand schematic reminder...
# [Apr 28]\--D-ESP 2-Year Birthday Celebration\!\!]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] \- first discussion of adaptive sampling strategies
# Mar 3 - CMORE Hawaii
# [Mar 10] \-\- wand schematic
# [Mar 17]
# [Mar 24]
# Mar 31 - team deploying MOE at M0; Brent at WHOI
# [Apr 7]
# [Apr 14]
# [Apr 21]\--wand schematic reminder...]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]

h4. &nbsp;


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
 
h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] \- first discussion of adaptive sampling strategies
# Mar 3 - CMORE Hawaii
# [Mar 10] \-\- wand schematic
# [Mar 17]
# [Mar 24]
# Mar 31 - team deploying MOE at M0; Brent at WHOI
# [Apr 7]
# [Apr 14]
# [Apr 21]\--wand schematic reminder...
# [Apr 28]\--D-ESP 2-Year Birthday Celebration\!\!&nbsp; (Poster is [^ESP Birthday Poster(smaller).pdf])]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] \- first discussion of adaptive sampling strategies
# Mar 3 - CMORE Hawaii
# [Mar 10] \-\- wand schematic
# [Mar 17]
# [Mar 24]
# Mar 31 - team deploying MOE at M0; Brent at WHOI
# [Apr 7]
# [Apr 14]
# [Apr 21]\--wand schematic reminder...
# [Apr 28]\--D-ESP 2-Year Birthday Celebration\!\!&nbsp; (Poster is [here])]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{panel:title=Administrative|borderColor=#0000ff}

h3. {color:#009900}[ESP Logos]{color}


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
{panel}

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h3. {color:#009900}[ESP Logos]{color}


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010]]></property>
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<property name="body"><![CDATA[# [2011 Science Meetings]
# [2011 Engineering Meetings]
# [2011 Software Development Meetings]]]></property>
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<property name="body"><![CDATA[h1. All dates 2010

# [Jan 5]
# [Feb 2]
# [Feb 9]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h2. {panel:title=_Administrative_|borderColor=#0000ff}



h3. {color:#009900}[ESP Logos]{color}


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
{panel}

h2. {panel:title=_Engineering_}


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4.


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}


h2. {panel:title=_Science_}

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010

{panel}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h2. {panel:title=_Administrative_|borderColor=#0000ff}

{panel}


h3. {color:#009900}[ESP Logos]{color}


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 4-29-2011.docx]

h2. {panel:title=_Engineering_}

{panel}


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. {panel:title=_Science_}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.&nbsp; Depth 5-9m.]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h2. {panel:title=_Administrative_|borderColor=#0000ff}



h3. {color:#009900}[ESP Logos]{color}


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]

{panel}

h2. {panel:title=_Engineering_}


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

{panel}

h2. {panel:title=_Science_}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}]]></property>
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<property name="body"><![CDATA[Present:&nbsp; Kevin, Chris P, Roman, Chris S, Elif, Jim, Bill

h3. Items:


h4. WHOI deployment

* Kevin returned from a GUI-development week, where he rec'd much positive feedback on ESP GUI.&nbsp; Many changes have been implemented.&nbsp; New version should be on Confluence by Friday.&nbsp; Older versions will then not work, as database structure has&nbsp; been changed.
* Complicated plans for ESP-Bruce recovery, depending on contingencies.&nbsp; Roman leaving May 21, to return June 11, unless he needs more time to run standards.&nbsp; This necessary as ESP-Bruce is giving very low numbers of _Alexandrium_\--more investigation needed as to why.&nbsp; Final plans will solidify as June 7 approaches.
* {color:#ff0000}ACTION ITEM{color}\-\- Chris S. to contact WHOI to have a final conference call discussing this swap on June 7 and the various contingencies.







h4. Other Items

* We will buy the 'suck-and-sniff' He leak detector.&nbsp; put on 900915.&nbsp; Roman will order.&nbsp;
* We will by optode for O2 sensing for D-ESP (see]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]
# [Apr 12] \-\- Roman at WHOI, Chris P Europe
# Apr 19
# [Apr 26]]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

# [Jan 4]
# [Jan 11]
# [Feb 8]
# [Feb 15]
# [Feb 22]
# Mar 1  \--CMORE Hawaii
# Mar 8  \--ad hoc mtg
# [Mar 15]
# [Mar 22] \--Discussion of G3
# [Mar 29]
# [Apr 5]
# [Apr 12] \-\- Roman at WHOI, Chris P Europe
# Apr 19
# [Apr 26]
# [May 10]]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h4. {panel:title=Administrative Items|BGcolor=blue|width=100%|borderWidth=4}

{panel}


h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]
{section}
{column:width=50%}

h4. {panel:title=Engineering|borderWidth=2}

{panel}


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{column}
{column:width=50%}

h4. {panel:title=Science|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
{panel}


h4. Collaboration Items

# [MFB-PCR distribution list] as of 4Nov2010
{column}
{section}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h4. {panel:title=Administrative Items|BGcolor=blue|width=100%|borderWidth=4}




h3. {color:#009900}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]
{panel}

{section}
{column:width=50%}

h4. {panel:title=Engineering|BGcolor=blue|borderWidth=4}




h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

{panel}
{column}
{column:width=50%}

h4. {panel:title=Science|BGcolor=blue|borderWidth=4}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]



h4. Collaboration Items

# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation. Done in three stages
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{jiraissues:https://oceana.mbari.org/jira/sr/jira.issueviews:searchrequest-xml/temp/SearchRequest.xml?&pid=10050&resolution=-1&component=10082&sorter/field=priority&sorter/order=DESC&tempMax=1000}
{panel}


]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation. Done in three stages
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
# [Development Log]
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{jiraissues:https://oceana.mbari.org/jira/sr/jira.issueviews:searchrequest-xml/temp/SearchRequest.xml?&pid=10050&resolution=-1&component=10082&sorter/field=priority&sorter/order=DESC&tempMax=1000}
{panel}


]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h2. {panel:title=_Administrative_|borderColor=#0000ff}




h3. {color:#009900}[ESP Logos]{color}


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]

{panel}

h2. {panel:title=_Engineering_}



h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}

h2. {panel:title=_Science_}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h2. {panel:title=_Administrative_|borderColor=#0000ff}

{panel}


h3. {color:#009900}[ESP Logos]{color}


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 5-12-2011.docx]

h2. {panel:title=_Engineering_}

{panel}


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]

h2. {panel:title=_Science_}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}]]></property>
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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] \- first discussion of adaptive sampling strategies
# Mar 3 - CMORE Hawaii
# [Mar 10] \-\- wand schematic
# [Mar 17]
# [Mar 24]
# Mar 31 - team deploying MOE at M0; Brent at WHOI
# [Apr 7]
# [Apr 14]
# [Apr 21]\--wand schematic reminder...
# [Apr 28]\--D-ESP 2-Year Birthday Celebration\!\!&nbsp; (Poster is [here|^ESP Birthday Poster(smaller).pdf])]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center


h2. {panel:title=_Administrative_|borderColor=#0000ff}




h3. {color:#009900}[ESP Logos]{color}


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 4-29-2011.docx]

{panel}

h2. {panel:title=_Engineering_}




h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]
# [Development Leads]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Deep ESP]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's] \- NEW -
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
h2. {panel:title=_Science_}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.&nbsp; Depth 5-9m.

{color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford. ]]></property>
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# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation. Done in three stages
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
# [Development Log]
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{jiraissues:https://oceana.mbari.org/jira/sr/jira.issueviews:searchrequest-xml/temp/SearchRequest.xml?&pid=10050&resolution=-1&component=10082&sorter/field=priority&sorter/order=DESC&tempMax=1000}
{panel}


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# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation. Done in three stages
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
# [Development Log]
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}


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<property name="body"><![CDATA[h1. All dates 2011

\\
# [Jan 6]
# [Jan 13]
# [Jan 20]
# [Feb 3]
# [Feb 10]
# [Feb 17]
# [Feb 24] \- first discussion of adaptive sampling strategies
# Mar 3 - CMORE Hawaii
# [Mar 10] \-\- wand schematic
# [Mar 17]
# [Mar 24]
# Mar 31 - team deploying MOE at M0; Brent at WHOI
# [Apr 7]
# [Apr 14]
# [Apr 21]\--wand schematic reminder...
# [Apr 28]\--D-ESP 2-Year Birthday Celebration\!\!&nbsp; (Poster is [here|^ESP Birthday Poster(smaller).pdf])
# May 5 \-\- Visit to ASU
# [May 12]]]></property>
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<property name="body"><![CDATA[Just a test]]></property>
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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation. Done in three stages
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{panel}
{blog-posts}
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{jiraissues:https://oceana.mbari.org/jira/sr/jira.issueviews:searchrequest-xml/temp/SearchRequest.xml?&pid=10050&resolution=-1&component=10082&sorter/field=priority&sorter/order=DESC&tempMax=1000}
{panel}


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# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation. Done in three stages
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{jiraissues:https://oceana.mbari.org/jira/sr/jira.issueviews:searchrequest-xml/temp/SearchRequest.xml?&pid=10050&resolution=-1&component=10082&sorter/field=priority&sorter/order=DESC&tempMax=1000}
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{panel}
{blog-posts}
{panel}


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<property name="body"><![CDATA[h2. 2010

# [Jan 28]]]></property>
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<property name="body"><![CDATA[\\
{tip:title=Who we purchased from:}

h2. American Portable Storage

Oakland, CA
1-800-838-4006&nbsp;&nbsp; &nbsp;(Ken)

+Rental Information+
220V single phase (newer; quiet)
Delivery/pickup $850
$650/mo w/ 2 mo min.&nbsp; Uses $95/mo electricity.

220V 3-phase
$600/mo.&nbsp; Older noisy.&nbsp; Uses $450/mo electricity.

{color:#ff0000}UPDATE on our{color} {color:#ff0000}{_}{+}purchase{+}{_}{color} {color:#ff0000}(2-25-2009){color}

Purchased 20' van, 220V Single Phase with 3hp refrigeration system, good from \-10 to 55F.&nbsp; SS sides, aluminum floor.


Michael McCurley--his quote is [here|^MBARI Quote.doc].
Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].
PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)
{tip}

h2. Aztec Containers

Stockton, CA
1-800-399-2126 (Mark)

220 3-phase
Delivery/pickup $495
$695/mo w/ 3 mo min.

h2. Refrigerated Container Services

Oakland, CA
1-510-568-9541

220 3-phase
delivery/pickup \~$500
$1000/mo w/ no minimum.

Could purchase for \~$7800.&nbsp; They may repurchase for ½ price after we're finished.

Reefers only have doors on one end.&nbsp; No lights.&nbsp; Pass-throughs?&nbsp; Unknown.]]></property>
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# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation. Done in three stages
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
# [Development Log]
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}


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# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation. Done in three stages
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
# [Development Log]
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}


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# Click on [GUI Web Start|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp] to launch the GUI application in Java Web Start
{panel}
{section}
{column:width=60%}
{panel:title=Goals Related to GUI|width=60%}
In the 2008/2009 proposals, the goals laid out that are related to the Graphical User Interface are:
# Develop a GUI and Data Management System (2007)
# Integrate GUI/DM system with ESP operations (2008)
# Transfer the ESP technology to groups outside of MBARI (2008 & 2009)
# Two major themes (2008/2009):
## Image analysis of the probe arrays
## Instrument State Visualization
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of teh instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument (or playback a mission run from a log file).
### Information is already logged but we need to convert that to a visual representation. Done in three stages
#### Build software to query instrument and/or use log and create instrument state vector
#### Determine COTS products to help with visualization
#### Purchase COTS and write software to depict the state vector as an animated ESP schematic
# Completion of graphical user interface and data management system for the ESP(2009)
{panel}
{column}
{column:width=40%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
{panel}
{panel:title=Design Documentation}
# [Requirements|Requirements (and Gathering) Documentation]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
# [Development Log]
{panel}
{column}
{section}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}


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<property name="body"><![CDATA[# Do we need to track the serial numbers of the pucks in the application?
# If we print barcodes on filters, do we want to track in the application?
# Does the delay (7 minutes) only happen at the beginning of each phase or each protocol?
# Is max duration at the phase level or protocol level?
]]></property>
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<property name="body"><![CDATA[This page details out the data model that exists in the database to back the object model.
!data model.jpg|align=centre!

h2. Notes

* I've written a basic CRUD test so I know that it can insert and delete trees of objects. Beyond that we'll have to work things out.
* At this point there is NO business logic implemented.  If a transaction breaks some database rule, for example, trying to insert a ConsumableAmount without a ConsumableType, an Exception will be thrown.
* Collections are lazy loaded but I haven't written any unit tests to verify that they're working.
* I had some issues with the ConsumableAmount table. It's a many-to-many join table with an extra column for storing a value. JPA *hates* that. (You have to have the primary keys for both the ConsumableType and PhaseType *BEFORE* inserting the ConsumableAmount; so ConsumableAmount would've need to be handled is separate transactions.) The workaround was to add an id column; it's not pretty but it works.
* All testing has been done against FOG. Is this copacetic or should I start setting up MySQL for developing against?
* All transactions are currently handled through a single EAO object.
* The ESP-DAL (<\- Data Access Layer) build uses Maven 2. A dependency graph is available at [here | ^ESP - Data Model Dependencies.png]

Kevin: Some questions I have about the model
* What sort of things go in Event_Types?  I think we are using those for mostly stuff that gets parsed out of the log file and stuffed into events, but should we have Protocol_Run, Phases, or Deployments in the event types even though they are actually subclasses?
* I think the Eventt hierarchy should look like Deployment->Phases->Protocol_Runs.  Just want to verify.]]></property>
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<property name="body"><![CDATA[h2. Notes

[~brian]: Here's a [UML of the current data model | ^Model Classes.jpg]. A few things to note:
* I color coded classes by related groups. Cascading transactions work within related groups only, e.g. deleting an instrument will delete all the associated yellow classes only. I haven't tested out all the Cascade relations yet, so deleting an image might delete your instrument to :-) . These should be easy fixes but I won't be able to write the tests until after my vacation sometime about 7/16.
* I've written a basic CRUD test so I know that it can insert and delete trees of objects. Beyond that we'll have to work things out.
* At this point there is NO buisness logic implemented.  If a transaction breaks some database rule, for example, trying to insert a ConsumableAmount without a ConsumableType, an Exception will be thrown.
* Collections are lazy loaded but I haven't written any unit tests to verify that they're working.
* I had some issues with the ConsumableAmount table. It's a many-to-many join table with an extra column for storing a value. JPA *hates* that. (You have to have the primary keys for both the ConsumableType and PhaseType *BEFORE* inserting the ConsumableAmount; so ConsumableAmount would've need to be handled is separate transactions.) The workaround was to add an id column; it's not pretty but it works.
* All testing has been done against FOG. Is this copacetic or should I start setting up MySQL for developing against?
* All transactions are currently handled through a single EAO object.
* The ESP-DAL (<\- Data Access Layer) build uses Maven 2. A dependency graph is available at [here | ^ESP - Data Model Dependencies.png]

Kevin: Some questions I have about the model
* What sort of things go in Event_Types?  I think we are using those for mostly stuff that gets parsed out of the log file and stuffed into events, but should we have Protocol_Run, Phases, or Deployments in the event types even though they are actually subclasses?
* I think the Eventt hierarchy should look like Deployment->Phases->Protocol_Runs.  Just want to verify.]]></property>
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<property name="body"><![CDATA[\\
{tip:title=Who we purchased from:}

h2. American Portable Storage

Oakland, CA
1-800-838-4006&nbsp;&nbsp; &nbsp;(Ken)

+Rental Information+
220V single phase (newer; quiet)
Delivery/pickup $850
$650/mo w/ 2 mo min.&nbsp; Uses $95/mo electricity.

220V 3-phase
$600/mo.&nbsp; Older noisy.&nbsp; Uses $450/mo electricity.

{color:#ff0000}UPDATE on our{color} {color:#ff0000}{_}{+}purchase{+}{_}{color} {color:#ff0000}(2-25-2009){color}
Michael McCurley--his quote is [here|^MBARI Quote.doc].
Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].
PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)
{tip}

h2. Aztec Containers

Stockton, CA
1-800-399-2126 (Mark)

220 3-phase
Delivery/pickup $495
$695/mo w/ 3 mo min.

h2. Refrigerated Container Services

Oakland, CA
1-510-568-9541

220 3-phase
delivery/pickup \~$500
$1000/mo w/ no minimum.

Could purchase for \~$7800.&nbsp; They may repurchase for ½ price after we're finished.

Reefers only have doors on one end.&nbsp; No lights.&nbsp; Pass-throughs?&nbsp; Unknown.]]></property>
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<property name="body"><![CDATA[Here is the information for the data model that was created to back the information needed in the GUI.]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]
# [Functional Requirements for Gen 3 ESP]

h4. &nbsp;


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
 
h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]]]></property>
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<property name="body"><![CDATA[&nbsp;Present:&nbsp; Jim, Roman, Chris P, Bill


Absent:&nbsp; Chris S., Julie, John
\\

h1.


h1. Papers
\\

h4. &nbsp;John & Roman

* John will combine Sept '07 and Oct '08 data.&nbsp; Currently combing through AUV, DA, and HAB data.&nbsp; Chris P. says all physical data for these deployments is in SigmaPlot and she can show Roman how to access.
* After Betty is up and running, and Bruce Keafer is gone, Roman can hit this full-time.

h4.
Chris P./ PCR paper


* Currently picking data out of notebooks, mainly the NEO m0 deployment of May '09 (Nov '08 pulled reagent from wrong valve; data suspect)
* {color:#cc0000}Next week{color}:&nbsp; skeleton outline/figure ideas/holes to fill/which journal.
* Chris sent out her summary of the water quality monitoring work in a Jan 17, 2010 email.

h1. Lab Issues

* Chris reading PICARD manual (new PCR machine).&nbsp; waiting for a loaner PC from Zorba who is on vacation.
* Bruce K. arrives Monday
** Roman will show him how to run ESP--will use Bruce/Mack
** Shannon Johnson will also shadow
** Roman needs Cheri to clear Bruce for operation (done 2-4-2010)

* Bruce has had software rolled back to Oct '08 and will rerun the DA assays; should be finished by Tuesday
* Cheri to look into a light-proof curtain wrap around Bruce so we don't miss pictures.&nbsp; Maybe check with Haddock lab on how to do this.
* Next week Girguis sending two grad students and Victoria Orphan sending 1 tech to learn how to run MFB.

h5. Betty

* has a full carousel
* will start mission on Weds
* over weekend it will sleep, then hammer next week (30 min break b/w runs)
* If it fails, we note detailed documentation on how we recover.&nbsp; Cheri needed here.
* Then---SCIENCE CHECKOUT---Cheri needs to shadow to learn this for the McLane build checkout.
*** bag reagents
*** load them
*** run tests (projected to take 3 days)
***# make lysate
***# make an array
***# run a phase&nbsp;
* need cell cultures to do this properly; McLane does not have.&nbsp; Might have to work with Bruce at WHOI.

h5. Moe

* &nbsp;waiting for Julie to get back

h4. Gordon

* &nbsp;Looks like PCR reagents are fine when running standards.&nbsp; 1 m/m line had bubble; IPC primer was also pulling funny.&nbsp; Chris found inhibition from normal samples, though.
* &nbsp;\\]]></property>
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<property name="body"><![CDATA[&nbsp;Present:&nbsp; Jim, Roman, Chris P, Bill
Absent:&nbsp; Chris S., Julie, John

h1. Papers


h4. &nbsp;John & Roman

* John will combine Sept '07 and Oct '08 data.&nbsp; Currently combing through AUV, DA, and HAB data.&nbsp; Chris P. says all physical data for these deployments is in SigmaPlot and she can show Roman how to access.
* After Betty is up and running, and Bruce Keafer is gone, Roman can hit this full-time.

h4.


h4. Chris P./ PCR paper

* Currently picking data out of notebooks, mainly the NEO m0 deployment of May '09 (Nov '08 pulled reagent from wrong valve; data suspect)
* {color:#cc0000}Next week{color}:&nbsp; skeleton outline/figure ideas/holes to fill/which journal.
* Chris sent out her summary of the water quality monitoring work in a Jan 17, 2010 email.

h1. Lab Issues

* Chris reading PICARD manual (new PCR machine).&nbsp; waiting for a loaner PC from Zorba who is on vacation.
* Bruce K. arrives Monday
** Roman will show him how to run ESP--will use Bruce/Mack
** Shannon Johnson will also shadow
** Roman needs Cheri to clear Bruce for operation (done 2-4-2010)

* Bruce has had software rolled back to Oct '08 and will rerun the DA assays; should be finished by Tuesday
* Cheri to look into a light-proof curtain wrap around Bruce so we don't miss pictures.&nbsp; Maybe check with Haddock lab on how to do this.
* Next week Girguis sending two grad students and Victoria Orphan sending 1 tech to learn how to run MFB.

h5. Betty

* has a full carousel
* will start mission on Weds
* over weekend it will sleep, then hammer next week (30 min break b/w runs)
* If it fails, we note detailed documentation on how we recover.&nbsp; Cheri needed here.
* Then-\--SCIENCE CHECKOUT-\--Cheri needs to shadow to learn this for the McLane build checkout.
*** bag reagents
*** load them
*** run tests (projected to take 3 days)
***# make lysate
***# make an array
***# run a phase&nbsp;
* need cell cultures to do this properly; McLane does not have.&nbsp; Might have to work with Bruce at WHOI.

h5. Moe

* &nbsp;waiting for Julie to get back

h4. Gordon

* &nbsp;Looks like PCR reagents are fine when running standards.&nbsp; 1 m/m line had bubble; IPC primer was also pulling funny.&nbsp; Chris found inhibition from normal samples, though.
* &nbsp;
\\]]></property>
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# [Jan 5]
# [Jan 12]]]></property>
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<property name="body"><![CDATA[[|ESPAPP:Betty|Software Revision Level of Betty]
[|ESPAPP:Bruce|Software Revision Level of Bruce]
[|ESPAPP:Moe|Software Revision Level of Moe]
[|ESPAPP:Gordon|Software Revision Level of Gordon]
[|ESPAPP:NEO|Software Revision Level of NEO]]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]
{quote}
{color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford. ]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg]; [Photo 2|^MBA_ESP_NEO 004.jpg]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]
{quote}
{color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford. ]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
{quote} Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sending boat out for look on May 18. {quote}
{color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford. ]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg]; [Photo 2|^MBA_ESP_NEO 004.jpg];
{quote}
{color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford. ]]></property>
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<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].
{quote}
{color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford. ]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">16777472</id>
</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">16810245</id>
<property name="body"><![CDATA[h2. +These are deployments during 2011 arranged chronologically+ (colors are same deployment)

\\  {color:#ff6666}Jan 4, 2011{color}\-\- Recover D-ESP from MARS

{color:#3300ff}&nbsp;March 31, 2011{color} \-\- Deploy Moe w/PCR to M0 (ISUS and CTD).&nbsp; This deployment to test adaptive sampling and overlaps with Kana and CANON Apr 18-29.

April 1 \-\- ship ESP Bruce (no PCR) to WHOI.

{color:#00cc00}April 19{color} \-\- ESP-Bruce (no PCR, no ISUS, but with accelerometers) deployed at 43' 2.074" N, 70' 36.828"W.  Depth 5-9m.
{quote}
Lost communication sometime b/w 8-9am EST on May 17.
Iridium tracker checked, and it stopped transmitting May 11.
Sent boat out for look on May 18. Found buoy, but note radar deflector sausage is missing [here|^DSCN1320.jpg|Buoy photo #1] and [here|^DSCN1299.jpg|Buoy photo #2].

Sunday, May 22 rec'd following email:

{color:#996600}Hello Monterey Bay Aquarium Research Institute:{color}
{color:#996600}&nbsp;{color}
{color:#996600}I just wanted to let you know that one of your research ESP NEO buoys washed up on Crane Beach in Ipswich, Massachusetts (42 41'07.48"N, 70 45'46.21"W), found&nbsp; 8:00 am (eastern time) this morning (5/22/2011), see attached photos.&nbsp; The equipment attached&nbsp; to the buoy did not appear to be damaged.&nbsp; I notified personnel at The Trustees of Reservation, owners of the property (thetrustees.org), and they said they would go out and retrieve the buoy.{color}
{color:#996600}&nbsp;{color}
{color:#996600}There was no PI contact listed on the buoy, and I couldn't find any information about ESP NEO on your website. So, I'm emailing the three of you assuming you would know who in your group oversees the project and equipment.{color}
{color:#996600}&nbsp;{color}
{color:#996600}\-Rob Vincent{color}
{color:#996600}rvincent13@gmail.com{color}
{color:#996600}603-828-5316{color}&nbsp;&nbsp;

Photos of damage taken by Rob Vincent:&nbsp; [Photo 1|^MBA_ESP_NEO 005.jpg|Buoy from bottom]; [Photo 2|^MBA_ESP_NEO 004.jpg|Radio]; [Photo 3|^MBA_ESP_NEO 002.jpg|Buoy name]; [Photo 4|^MBA_ESP_NEO 001.jpg|Buoy side]

May 23.&nbsp; Attempted recovery of ESP.&nbsp; Message from Roman:

&nbsp;&nbsp;&nbsp; We went out to the site where espbruce was moored and attempted to find it.&nbsp; The weather was very poor and water was very turbid.&nbsp; Using the ships depth finder we found a promising target.&nbsp; In difficult conditions the divers performed a search but espbruce was not found.
&nbsp;&nbsp;&nbsp; We recovered the mooring.&nbsp; It looks like the cable was pulled straight out of the cone.&nbsp; The top mast is bent but I cannot say if this was caused by a rough landing on the beach or boat impact.&nbsp; There are no dents or gouges on the mooring.&nbsp; The radio box is dry and antenna looks ok.
&nbsp;&nbsp;&nbsp; Thursday the RV Gulf Challenger may be able to survey the area with a side scanning sonar.&nbsp; This will be a much better way to search for espbruce.&nbsp;
{quote}\\ \\

{color:#3300ff}May 2{color} \-\- Recover MOE from M0 on Zephyr.&nbsp; Also recovered in-situ incubators for Stanford. ]]></property>
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<property name="body"><![CDATA[h2. 2010

# [Jan 14] ]]></property>
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<id name="id">11272403</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirements]
# [Detection Technologies]

h4. &nbsp;


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [Functional Requirements for Gen 3 ESP]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]]]></property>
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<id name="id">11272389</id>
<property name="body"><![CDATA[h4. Requirement Documents

# Project overview

h4. Detection Technologies
\\ \\]]></property>
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<id name="id">11272390</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [Functional Requirements for Gen 3 ESP]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]]]></property>
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<property name="body"><![CDATA[h4. Requirements

# Project overview

h4.

\\
\\]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">11272398</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]

h2. Engineering


h4. &nbsp;Generation 3

# [Requirement]
# [Detection Technologies]

h4. &nbsp;


h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Task Wish List between D-ESP deployments 27OCT--25NOV, 2009]
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]
h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [Functional Requirements for Gen 3 ESP]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]]]></property>
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</property>
</object>
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<id name="id">22544386</id>
<property name="body"><![CDATA[Materials for Accel cartridge testing
# [Cartridge assembly document from Accel|^Cartage Assembly Procedure.docx|cartridge build procedure]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">22511618</id>
</property>
</object>
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<id name="id">31850498</id>
<property name="body"><![CDATA[h2.


h2. Scott Creek eDNA

{color:#ff00ff}March 25, 2019{color} \--&nbsp; Deploy ESP-Waldo at Scott creek with 132 archival pucks.&nbsp; Initially will sample 3 times/day (6am 12pm 6pm), but that will change.&nbsp; Powered by Jensen's homegrown solar array.


h2. \\
\\]]></property>
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<id name="id">10387531</id>
<property name="body"><![CDATA[\\

h2. American Portable Storage

Oakland, CA
1-800-838-4006&nbsp;&nbsp; &nbsp;(Ken)

220V single phase (newer; quiet)
Delivery/pickup $850
$650/mo w/ 2 mo min.&nbsp; Uses $95/mo electricity.

220V 3-phase
$600/mo.&nbsp; Older noisy.&nbsp; Uses $450/mo electricity.

{color:#ff0000}UPDATE (2-25-2009){color}
{color:#0000ff}{*}THIS IS THE COMPANY WE PURCHASED FROM.*{color}

Michael McCurley--his quote is [here|^MBARI Quote.doc].

Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].
PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)

h2. Aztec Containers

Stockton, CA
1-800-399-2126 (Mark)

220 3-phase
Delivery/pickup $495
$695/mo w/ 3 mo min.

h2. Refrigerated Container Services

Oakland, CA
1-510-568-9541

220 3-phase
delivery/pickup \~$500
$1000/mo w/ no minimum.

Could purchase for \~$7800.&nbsp; They may repurchase for ½ price after we're finished.

Reefers only have doors on one end.&nbsp; No lights.&nbsp; Pass-throughs?&nbsp; Unknown.]]></property>
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<property name="body"><![CDATA[\\
{tip:title=Who we Chose}
h2. American Portable Storage

Oakland, CA
1-800-838-4006&nbsp;&nbsp; &nbsp;(Ken)

220V single phase (newer; quiet)
Delivery/pickup $850
$650/mo w/ 2 mo min.&nbsp; Uses $95/mo electricity.

220V 3-phase
$600/mo.&nbsp; Older noisy.&nbsp; Uses $450/mo electricity.

{color:#ff0000}UPDATE (2-25-2009){color}

Michael McCurley--his quote is [here|^MBARI Quote.doc].

Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].
PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)

{tip}
h2. Aztec Containers

Stockton, CA
1-800-399-2126 (Mark)

220 3-phase
Delivery/pickup $495
$695/mo w/ 3 mo min.

h2. Refrigerated Container Services

Oakland, CA
1-510-568-9541

220 3-phase
delivery/pickup \~$500
$1000/mo w/ no minimum.

Could purchase for \~$7800.&nbsp; They may repurchase for ½ price after we're finished.

Reefers only have doors on one end.&nbsp; No lights.&nbsp; Pass-throughs?&nbsp; Unknown.]]></property>
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<property name="body"><![CDATA[\\
{tip:title=Who we Chose}

h2. American Portable Storage

Oakland, CA
1-800-838-4006&nbsp;&nbsp; &nbsp;(Ken)

220V single phase (newer; quiet)
Delivery/pickup $850
$650/mo w/ 2 mo min.&nbsp; Uses $95/mo electricity.

220V 3-phase
$600/mo.&nbsp; Older noisy.&nbsp; Uses $450/mo electricity.

{color:#ff0000}UPDATE (2-25-2009){color}
Michael McCurley--his quote is [here|^MBARI Quote.doc].
Pictures of how to hook-up electrical are [here|^ElectricHookup.jpg].&nbsp; Here is the [junction box|^ControllerJunctionBox1.jpg].&nbsp; Here is how to [start the unit|^StartingtheUnit.jpg].
PDF files of the van specifications and structural drawings are in the "STORAGE VAN MATERIAL"&nbsp; [folder|cifs://tornado.shore.mbari.org/projectlibrary/ESP/]. (this is still under construction, but it's in the project library)
{tip}

h2. Aztec Containers

Stockton, CA
1-800-399-2126 (Mark)

220 3-phase
Delivery/pickup $495
$695/mo w/ 3 mo min.

h2. Refrigerated Container Services

Oakland, CA
1-510-568-9541

220 3-phase
delivery/pickup \~$500
$1000/mo w/ no minimum.

Could purchase for \~$7800.&nbsp; They may repurchase for ½ price after we're finished.

Reefers only have doors on one end.&nbsp; No lights.&nbsp; Pass-throughs?&nbsp; Unknown.]]></property>
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<property name="body"><![CDATA[h3. Administrative

# [MFB 2007-08 Timeline |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Timeline/MFB%20PCR%20Timeline.doc]
# [MFB Users Manual v1.7|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Users%20Manual/MFB%20Users%20Manual%20V1_7%2010_03_2008.doc]

h3. &nbsp;Fluidics Construction

# [Fluidics Tubing Diagram |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/Fluidics/MFB_Fluidics_diagram4-22-08.ppt]
# [Redesigned ASV |http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/ASV%20modification_SPE_extract_11_07.ppt]
# [MFB Parts List|http://mww.mbari.org/ProjectLibrary/ESP/Micro%20Fluidic%20Block/BOM/MFB%20Parts%20List%2020070920.xls]

]]></property>
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<id name="id">10387524</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [4K Sphere]
# [4k Deep Water Sampling Module (DWSM)]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
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<id name="id">10387526</id>
<property name="body"><![CDATA[# [Comments from July 9, 2008 Design Review]
# [Doug's collected comments of 9 july CDR]

* [The DWSM scheme |DWSM Deep Water Sampling Module^4k DWSM Operation.ppt] (in particular see slide #3)]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387525</id>
<property name="body"><![CDATA[# [Comments from July 9, 2008 Design Review]
# [Doug's collected comments of 9 july CDR]

* [The DWSM scheme |^4k DWSM Operation.ppt] (in particular see slide #3)]]></property>
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</element>
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<property name="version">1</property>
<property name="creatorName"><![CDATA[brent]]></property>
<property name="creationDate">2008-10-30 19:01:04.887</property>
<property name="lastModifierName"><![CDATA[brent]]></property>
<property name="lastModificationDate">2008-10-30 19:01:04.887</property>
<property name="versionComment"><![CDATA[]]></property>
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<property name="contentStatus"><![CDATA[current]]></property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387527</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [4K Sphere]
# [DWSM: 4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
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</property>
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<id name="id">10387529</id>
<property name="body"><![CDATA[# [Notes from delivery of 3rd module (April 1, 2009)]]]></property>
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<property name="body"><![CDATA[This page lists some terminology and their definitions and context as they were used in the design work of the GUI application.  This is to ensure that when discussions are occurring, we are all talking about the same thing.
||Term||Definition||
|+*Mission*+|This is a logical span of time in which an ESP instrument is operating which has some start and end time.  It is usually associated with a the deployment and recovery of an ESP and consists of a sequence of phases.|
|+*Deployment*+|Is used synonymously with *Mission*|
|+*Mission Script*+|An ASCII file that contains Ruby commands that tell the ESP what actions to take at what times.|
|+*Phase*+|Consists of a cycle of instrument power up, a sequence of one or more protocol runs, and a power down.  Examples of phases are HAB, BAC, LARV, etc.  The concept of a phase is important as a mission script is defined using phases.  Phases can contain protocol run sequences that will take more than one sample of water. i.e. The relationship between phase and sample is one-to-many.|
|+*Sample Volume*+|A volume of water that is drawn into the instrument that contains the organisms which the instrument is attempting to identify.  More than one protocol run can use the water from one sample.  This means the relationship between sample and protocol runs is one-to-many.|
|+*Protocol Run*+|Also just called _protocol_ or _assay_. Some named chemical protocol that yields data we wish to log. Each protocol run will have one puck, one filter and many images.|
|+*Puck*+|Metal ring that holds filter paper which is used to capture and process organisms|
|+*Filter*+|Special paper that is printed with various materials to help in detection of organisms. Not all filters have probes on them (for example, WCR has not probes as it just archives the organisms)|
|+*GAL File*+|File that is produced by the filter printer and contains the locations in X,Y coordinates and what probes are at those X,Y coordinates|
|+*Probe*+||
|+*SH*+|Acronym for Sandwich Hybridization|
|+*Standard Curve*+|A curve that maps intensity to density of organisms.  You use it to take the intensity of an image and calculate the density of organisms in the sample|
|+*Consumable*+|Is any resources on the instrument that can be consumed.  Examples are:
# Power
# Reagants
# Capacities like waste (there are 2)|
]]></property>
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<property name="body"><![CDATA[This page lists some terminology and their definitions and context as they were used in the design work of the GUI application.  This is to ensure that when discussions are occurring, we are all talking about the same thing.
||Term||Definition||
|+*Mission*+|This is a logical span of time in which an ESP instrument is operating which has some start and end time.  It is usually associated with a the deployment and recovery of an ESP and consists of a sequence of phases.|
|+*Deployment*+|Is used synonymously with *Mission*|
|+*Mission Script*+|An ASCII file that contains Ruby commands that tell the ESP what actions to take at what times.|
|+*Phase*+|Consists of a cycle of instrument power up, a sequence of one or more protocol runs, and a power down.  Examples of phases are HAB, BAC, LARV, etc.  The concept of a phase is important as a mission script is defined using phases.  Phases can contain protocol run sequences that will take more than one sample of water. i.e. The relationship between phase and sample is one-to-many.|
|+*Sample Volume*+|A volume of water that is drawn into the instrument that contains the organisms which the instrument is attempting to identify. The volume of water is never actually stored in the instrument, it is run directly through a puck and filter and then sent to waste.|
|+*Lysate*+|A solution that is created by adding a solvent to the material that is filter out of the sample water by the filter.  This solution is then used as the source for protocol runs (and other).  In other words the lysate can be split amongst many protocol runs (and other events)|
|+*Protocol Run*+|Also just called _protocol_ or _assay_. Some named chemical protocol that yields data we wish to log. Each protocol run will have one puck, one filter and many images.|
|+*Puck*+|Metal ring that holds filter paper which is used to capture and process organisms|
|+*Filter*+|Special paper that is printed with various materials to help in detection of organisms. Not all filters have probes on them (for example, WCR has not probes as it just archives the organisms)|
|+*GAL File*+|File that is produced by the filter printer and contains the locations in X,Y coordinates and what probes are at those X,Y coordinates|
|+*Probe*+||
|+*SH*+|Acronym for Sandwich Hybridization|
|+*Standard Curve*+|A curve that maps intensity to density of organisms.  You use it to take the intensity of an image and calculate the density of organisms in the sample|
|+*Consumable*+|Is any resources on the instrument that can be consumed.  Examples are:
# Power
# Reagants
# Capacities like waste (there are 2)|
]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketd by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}

h3. Important log entries
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
."Qmail"HABfans.email "Can@22:44:45, 22.0C, 12% humidity, 14.8psia, 15.744V, 0.384A, 0.390A avg, 6.04W\\nCTD@22:45:23, 22.0495C, 0.010 decibars, 0.0000 S/m, -1.58 mg/m^3, 94.76%, 0.215 1/m\\nISUS@22:45:46, 12.350 uM/L no^3, -1.000 uM/L hs, 32.5700 psu",:Subject=>"hab sampling at most 100.0ml, wcr at most 50.0ml"
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
#\PuckCamera: snap -bin=2,2 40 /var/log/esp/hab08oct0700h100ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/hab08oct0700h100ml.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
."Qmail"HABfans.email "56.113 sec auto-exposure",:Subject=>"hab08oct0700h100ml images!"
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"

#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"

#"brent 7096"\Session Begun
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}

h3. Important log entries
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
."Qmail"HABfans.email "Can@22:44:45, 22.0C, 12% humidity, 14.8psia, 15.744V, 0.384A, 0.390A avg, 6.04W\\nCTD@22:45:23, 22.0495C, 0.010 decibars, 0.0000 S/m, -1.58 mg/m^3, 94.76%, 0.215 1/m\\nISUS@22:45:46, 12.350 uM/L no^3, -1.000 uM/L hs, 32.5700 psu",:Subject=>"hab sampling at most 100.0ml, wcr at most 50.0ml"
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
#\PuckCamera: snap -bin=2,2 40 /var/log/esp/hab08oct0700h100ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/hab08oct0700h100ml.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
."Qmail"HABfans.email "56.113 sec auto-exposure",:Subject=>"hab08oct0700h100ml images!"
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"

#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"

#"brent 7096"\Session Begun
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}]]></property>
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<id name="id">10387542</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketed by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can environmental data is combined with ancillary instrument data in a single log entry that is separated by escaped new lines.  An example:
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}

h3. Important log entries
{noformat}
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
."Qmail"HABfans.email "Can@22:44:45, 22.0C, 12% humidity, 14.8psia, 15.744V, 0.384A, 0.390A avg, 6.04W\\nCTD@22:45:23, 22.0495C, 0.010 decibars, 0.0000 S/m, -1.58 mg/m^3, 94.76%, 0.215 1/m\\nISUS@22:45:46, 12.350 uM/L no^3, -1.000 uM/L hs, 32.5700 psu",:Subject=>"hab sampling at most 100.0ml, wcr at most 50.0ml"
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
#\PuckCamera: snap -bin=2,2 40 /var/log/esp/hab08oct0700h100ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/hab08oct0700h100ml.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
."Qmail"HABfans.email "56.113 sec auto-exposure",:Subject=>"hab08oct0700h100ml images!"
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"

#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"

#"brent 7096"\Session Begun
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
{gliffy:name=Normal Log Flow|space=ESPAPP|page=Parsing the Raw ESP Log File Format|pageid=8912932|align=left|size=L}]]></property>
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<property name="body"><![CDATA[This page lists some terminology and their definitions and context as they were used in the design work of the GUI application.  This is to ensure that when discussions are occurring, we are all talking about the same thing.
||Term||Definition||
|+*Mission*+|This is a logical span of time in which an ESP instrument is operating which has some start and end time.  It is usually associated with a the deployment and recovery of an ESP.|
|+*Protocol Run*+|Also just called _protocol_. A sequence of steps (think recipe) that the ESP goes through to achieve a specific goal. Each protocol run will have one puck and filter|
|+*Phase*+|Is a sequence of protocol runs that.  Examples of phases are HAB, BAC, LARV.  The concept of a phase is important as a mission script is defined using phases.  Phases can contain protocol sequence that will take more than one sample of water. i.e. The relationship between phase and sample is one-to-many.|
|+*Deployment*+|Is used synonymously with *Mission*|
|+*Mission Script*+|An ASCII file that contains Ruby commands that tell the ESP what actions to take at what times|
|+*Puck*+|Metal ring that holds filter paper which is used to capture and process organisms|
|+*Filter*+|Special paper that is printed with various materials to help in detection of organisms. Not all filters have probes on them (for example, WCR has not probes as it just archives the organisms)|
|+*Probe*+||
|+*SH*+|Acronym for Sandwich Hybridization|
|+*GAL File*+|File that is produced by the filter printer and contains the locations in X,Y coordinates and what probes are at those X,Y coordinates|
|+*Standard Curve*+|A curve that maps intensity to density of organisms.  You use it to take the intensity of an image and calculate the density of organisms in the sample|
|+*Sample Volume*+|A volume of water that is brought into the instrument that contains the organisms which the instrument is attempting to identify|
|+*Consumable*+|Is any resources on the instrument that can be consumed.  Examples are:
# Power
# Reagants
# Capacities like waste (there are 2)|
]]></property>
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<property name="body"><![CDATA[h3. Machine Builds

* Bruce has been run a lot and can't reproduce the processing error
* Seems to be an accumulation of something in the software (27May\--happening on Neo during deployment-\-more evidence it's software and not dwarf)
* HANDS
** Gordon's goes at 50% force (old ones worked at 30%)
** Betty taking 70% but with new frame works better than Gordon.

h3. MFB


h3. Drifter

* Test tank tomorrow (Friday).
* Dive days moved to 27 and 28 next week. Likely will only use the 27th.
* There will be no tension control on winch for June dive.
* Pressure transducer and moxa need mounting on lid
** need fitting and adaptor using power port on lid
** Mike P to make bracket for MOXA
** Roman to move mooring to high bay; Jim to get Ken Smith batteries
* Gene wants ESP 100lbs negative.&nbsp; Will work with Mike to accomplish.
* BRUCE is going in drifter

h3. Software

* &nbsp;

h3. Deep ESP


h6.

* Wand; don't have cables long enough for long wand assembly.&nbsp; Cables arrive 29th (too late)
* Will shoot for a 3' stubby.&nbsp; Code still to be developed
* TSV--needed tightening
* CPLD code works but needs testing
* Mink is soldered and waiting for modem before potting.
* D-ESP cleaning
** Doug has two 4" sections that can't be cleaned with toxicant.&nbsp; So idea is to add a filter puck taht we push tox through the core to clean both those lines in DWSM, then go to next SH1 run.

h3. GUI

* Will be loaded on Gordon and Betty for beta testing.

h3. Deployment Issues

For June:
* Mack in sphere
* Bruce in Drifter
* Moe on bench&nbsp;

Here is the schedule for the next two weeks:
\\
\\
\\

h3. &nbsp;Other Items:

* need loaner computer from IS for summer student&nbsp; (Cheri will put in request with IS for what we need)
{gliffy:name=calendar|space=ESPAPP|page=21May2009|pageid=10354699|align=left|size=L}]]></property>
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<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center

{center:class=myclass}
{center}
{panel:title=Administrative Items|borderWidth=2}

h2. {color:#009955}[ESP Logos]{color}


h2. Meeting notes

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]
# [2010 Meeting Notes]
# [2011 Meeting Notes]
## [2011 calendar|^ESP 2011 calendar 8-08-2011.docx] (May-Sep, 2011)
# [2012 Meeting Notes]
# [2013 Meeting notes]
{panel}
{section}
{column:width=50%}
{panel:title=Engineering|borderWidth=2}

h4. &nbsp;Generation 3

# [Cartridge testing]
# [Functional Requirements for G3 ESP]
# [Detection Technologies]
# [Development Leads]
# [G3 - LRAUV Integration]
# [Lab Automation Conference Notes|ESPAPP:Lab Automation]
# [G3 Process Diagrams]
# [Turbine Technical Options|ESPAPP:G3 -Turbine- Technical Options]
# [G3 IO List|G3 IO list - Control loops]
# [AccelBiotech Slides|ESPAPP:AccelBiotech Slides]

h4. System Integration

# [System tubing diagram (updated 03 Nov 2009) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2003Nov09.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [EM cables], shockle, and line lengths
# [Deep ESP]/Sable Tracker
# [Melo Iridium Tracker]
# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [Sampling Wand Functional Req's]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]
# [ISUS issues] (updated 31 Aug 2010)
# [ESP Drifter]

h4. Software

# [Instrument Software Revision Level]
# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Application]
# [ESP Image Analysis Application]
# [ESP Image Analysis Automation]
# [ESP Servo Simulation]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]
# [CVS For McLane]
# [Helpful DEBUGGING commands to discern machine state]
{panel}
{column}
{column:width=50%}
{panel:title=Deployments|borderWidth=2}
# [2008 Deployments]
# [2009 Deployments]
# [2010 Deployments]
# [2011 Deployments]
## [JdF Straw Man Schedule|^Mission plan straw man.pdf|Schedule as of 5-26-2011]
# [2012 Deployments]
# [2013 Deployments]
# [2014 Deployments]
{panel}
{panel:title=Science|borderWidth=2}
# [Sandwich Hybridization Assay]
# [MFB-PCR distribution list] as of 4Nov2010
{panel}
{column}
{section}]]></property>
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<property name="body"><![CDATA[h3. Machine Builds

* Bruce has been run a lot and can't reproduce the processing error
* Seems to be an accumulation of something in the software (27May\--happening on Neo during deployment-\-more evidence it's software and not dwarf)
* HANDS
** Gordon's goes at 50% force (old ones worked at 30%)
** Betty taking 70% but with new frame works better than Gordon.

h3. MFB


h3. Drifter

* Test tank tomorrow (Friday).
* Dive days moved to 27 and 28 next week. Likely will only use the 27th.
* There will be no tension control on winch for June dive.
* Pressure transducer and moxa need mounting on lid
** need fitting and adaptor using power port on lid
** Mike P to make bracket for MOXA
** Roman to move mooring to high bay; Jim to get Ken Smith batteries
* Gene wants ESP 100lbs negative.&nbsp; Will work with Mike to accomplish.
* BRUCE is going in drifter

h3. Software

* &nbsp;

h3. Deep ESP


h6.

* Wand; don't have cables long enough for long wand assembly.&nbsp; Cables arrive 29th (too late)
* Will shoot for a 3' stubby.&nbsp; Code still to be developed
* TSV--needed tightening
* CPLD code works but needs testing
* Mink is soldered and waiting for modem before potting.
* D-ESP cleaning
** Doug has two 4" sections that can't be cleaned with toxicant.&nbsp; So idea is to add a filter puck taht we push tox through the core to clean both those lines in DWSM, then go to next SH1 run.

h3. GUI

* Will be loaded on Gordon and Betty for beta testing.

h3. Deployment Issues

For June:
* Mack in sphere
* Bruce in Drifter
* Moe on bench&nbsp;

Here is the schedule for the next two weeks:
\\
\\
\\

h3. &nbsp;Other Items:

* need loaner computer from IS for summer student&nbsp; (Cheri will put in request with IS for what we need)]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Details.

*Date*

What'd we do.

*Sept 25*]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing (i.e. Comments generated by the code can't be changed nilly-willy anymore)
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated and inconsistent format.  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# ]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

h4. {color:#ff00cc}Puget Sound{color}

_{+}Lummi Bay:+_

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)

*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.&nbsp; Subsequent investigation found that modem card had been cancelled with T-Mobile due to NOAA miscommunication.&nbsp; When new one was tried, operator did not know to 'close the door' on the modem in order to power the card.&nbsp; Brent flew up and fixed.&nbsp; Missed 4 days of sampling.

*August 18*\--Lummi Bay deployment ended.&nbsp; Machine returned to NOAA.

_{+}Samish Bay:&nbsp;+_

*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; No CTD.&nbsp; Both machines have MFB and PCR.&nbsp; Media event was July 18.

Aug 14--Recover Gordon

Aug 17--Deploy (swap) NEO.
\\

h4. {color:#ff00cc}ECOHAB/CANON--Monterey Bay{color}

*&nbsp;September 10, 2013*\-\- Deploy 2 ESP's in Monterey Bay.&nbsp; First time in southern part of bay.

'North'
ESP-Mack.&nbsp; Lat 36.9048, Long \-121.93659, Water depth 32m, Can depth 9.8m.

'South'
ESP-Bruce. Lat 36.63908, Long \-121.87884, Water depth 60m, Can depth 4.8m]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore)
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated and inconsistent format.  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note|title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketd by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop]]></property>
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<property name="body"><![CDATA[h4. {color:#ff00cc}ECOHAB/CANON--So. California{color}

*March 7, 2013*

Rented 12' open U-Haul trailer loaded with all mooring gear.&nbsp; Pulled with F-350 passenger van.

Outer Shelf (~5 miles offshore)
ESP-Bruce, CTD w/ optode, no ISUS.&nbsp; Only running HAB/DA
At 10:15am on March 7, 2013, water depth was 52.5m.
Top of can as measured by divers was 24m
Boat position at deployment:&nbsp; 33.58553&nbsp; \-118.03752
Melo satellite tracker position 33.58542 \-118.03747 (IMEI #300234060014550)

In-shore (~3 miles offshore)
ESP-Mack, CTD w/ no optode, no ISUS.&nbsp; Only running HAB/DA
At 11:40am on March 7, 2013, water depth was 28m.
Top of can as measured by divers was 8.2m
Boat position at deployment:&nbsp; 33.60612&nbsp; \-118.02133
Melo satellite tracker position 33.60621 \-118.0214&nbsp; (IMEI #300034012090780)

Minor problem with comms upon deployment; difficulty establishing a connection.&nbsp; Seems to have 'fixed' itself.

&nbsp;Divers:&nbsp; Eric Castillo, Steve Lang, and Andrew Solomon

*April 3, 2013*\--Mack's heater fails to respond.&nbsp; Full current but no  temperature increase.&nbsp; Mission over.&nbsp; Try to salvage some runs by  running final filters as 'archives'...

*April 7, 2013*\--Bruce started having sticky puck issuses, and  on this day we lost comm's to the instrument.&nbsp; MELO reports it's still  in position, but there is no communication.&nbsp; Mission ended.

*&nbsp;April 11, 2013*\--Recovered both instruments.&nbsp; Returned to MBARI via flatbed.

Dives:&nbsp; Eric Castillo, Steve Lang, Chris Glaeser
\\

h4. {color:#ff00cc}D-ESP on MARS cable{color}

*April 18, 2013*\--Deployed D-ESP with CTD, ISMS, and Sediment trap.&nbsp; First sample successfully fired on April 19.&nbsp;

h4. {color:#ff00cc}Puget Sound{color}

_{+}Lummi Bay:+_

*June 20, 2013*\--Deployed Univ. British Columbia ESP at the Lummi Bay aquaculture site.&nbsp; Data streamed here:

[http://www.nwfsc.noaa.gov/research/divisions/efs/microbes/harmful_algae/lummi_live_data.cfm]

*July 19, 2013*\--Recovered UBC ESP from Lummi (called ESPubc)

*July 21*\--Deploy NOAA ESP at Lummi (called ESPFriday).&nbsp; Lost comms to this machine on Aug 1.&nbsp; Annie going to investigate.&nbsp; Subsequent investigation found that modem card had been cancelled with T-Mobile due to NOAA miscommunication.&nbsp; When new one was tried, operator did not know to 'close the door' on the modem in order to power the card.&nbsp; Brent flew up and fixed.&nbsp; Missed 4 days of sampling.

*August 18*\--Lummi Bay deployment ended.&nbsp; Machine returned to NOAA.

_{+}Samish Bay:&nbsp;+_

*July 16, 2013*\--Deploy MBARI ESP-Gordon at Samish bay @ Taylor Shellfish Farm.&nbsp; No CTD.&nbsp; Both machines have MFB and PCR.&nbsp; Media event was July 18.

Aug 14--Recover Gordon

Aug 17--Deploy (swap) NEO.

Sep 10--processing syringe servo motor has failed.&nbsp; Decision to run out remaining mission with archive only.

Sep 16--NEO's mission ends.&nbsp; NOAA to recover and Roman/Kevan retrieved both machines Sep 25.


h4. {color:#ff00cc}ECOHAB/CANON--Monterey Bay{color}

*&nbsp;September 10, 2013*\-\- Deploy 2 ESP's in Monterey Bay.&nbsp; First time in southern part of bay.

'North'
ESP-Mack.&nbsp; Lat 36.9048, Long \-121.93659, Water depth 32m, Can depth 9.8m.

'South'
ESP-Bruce. Lat 36.63908, Long \-121.87884, Water depth 60m, Can depth 4.8m]]></property>
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<id name="id">10387486</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.]]></property>
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<id name="id">10387475</id>
<property name="body"><![CDATA[h3. Machine Builds

* Bruce has been run a lot and can't reproduce the processing error
* Seems to be an accumulation of something in the software (27May\--happening on Neo during deployment-\-more evidence it's software and not dwarf)
* HANDS
** Gordon's goes at 50% force (old ones worked at 30%)
** Betty taking 70% but with new frame works better than Gordon.

h3. MFB


h3. Drifter

* Test tank tomorrow (Friday).
* Dive days moved to 27 and 28 next week. Likely will only use the 27th.
* There will be no tension control on winch for June dive.
* Pressure transducer and moxa need mounting on lid
** need fitting and adaptor using power port on lid
** Mike P to make bracket for MOXA
** Roman to move mooring to high bay; Jim to get Ken Smith batteries
* Gene wants ESP 100lbs negative.&nbsp; Will work with Mike to accomplish.
* BRUCE is going in drifter

h3. Software

* &nbsp;

h3. Deep ESP


h6.

* Wand; don't have cables long enough for long wand assembly.&nbsp; Cables arrive 29th (too late)
* Will shoot for a 3' stubby.&nbsp; Code still to be developed
* TSV--needed tightening
* CPLD code works but needs testing
* Mink is soldered and waiting for modem before potting.
* D-ESP cleaning
** Doug has two 4" sections that can't be cleaned with toxicant.&nbsp; So idea is to add a filter puck taht we push tox through the core to clean both those lines in DWSM, then go to next SH1 run.

h3. GUI

* Will be loaded on Gordon and Betty for beta testing.

h3. Deployment Issues

For June:
* Mack in sphere
* Bruce in Drifter
* Moe on bench&nbsp;

\\
\\
\\

h3. &nbsp;Other Items:

* need loaner computer from IS for summer student&nbsp; (Cheri will put in request with IS for what we need)
Here is the schedule for the next two weeks:

* {gliffy:name=calendar\|space=ESPAPP\|page=21May2009\|pageid=10354699\|align=left\|size=L}]]></property>
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<property name="body"><![CDATA[Deployment 2 Neo.&nbsp; The processing dwarf bug (PDB) manifest today&nbsp; first processing syringe position error with reversal.&nbsp; After Cheri recover syringe&nbsp; then processing clamp errors out but is recovered.]]></property>
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</property>
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<id name="id">10387503</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketd by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}

h3. Important log entries
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 2\\nEnding Tue Oct 07 06:00:00 PDT 2008",:Subject=>"08oct06mack begun"
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
."Qmail"HABfans.email "Can@22:44:45, 22.0C, 12% humidity, 14.8psia, 15.744V, 0.384A, 0.390A avg, 6.04W\\nCTD@22:45:23, 22.0495C, 0.010 decibars, 0.0000 S/m, -1.58 mg/m^3, 94.76%, 0.215 1/m\\nISUS@22:45:46, 12.350 uM/L no^3, -1.000 uM/L hs, 32.5700 psu",:Subject=>"hab sampling at most 100.0ml, wcr at most 50.0ml"
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
#\PuckCamera: snap -bin=2,2 40 /var/log/esp/hab08oct0700h100ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/hab08oct0700h100ml.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
."Qmail"HABfans.email "56.113 sec auto-exposure",:Subject=>"hab08oct0700h100ml images!"
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"

#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"

#"brent 7096"\Session Begun
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore)
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated and inconsistent format.  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketd by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}

h3. Important log entries
{noformat}
."Qmail"GoodNews.email "Starting w/pucks in tube 2\\nEnding Tue Oct 07 06:00:00 PDT 2008",:Subject=>"08oct06mack begun"
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
."Qmail"HABfans.email "Can@22:44:45, 22.0C, 12% humidity, 14.8psia, 15.744V, 0.384A, 0.390A avg, 6.04W\\nCTD@22:45:23, 22.0495C, 0.010 decibars, 0.0000 S/m, -1.58 mg/m^3, 94.76%, 0.215 1/m\\nISUS@22:45:46, 12.350 uM/L no^3, -1.000 uM/L hs, 32.5700 psu",:Subject=>"hab sampling at most 100.0ml, wcr at most 50.0ml"
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
#\PuckCamera: snap -bin=2,2 40 /var/log/esp/hab08oct0700h100ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/hab08oct0700h100ml.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
."Qmail"HABfans.email "56.113 sec auto-exposure",:Subject=>"hab08oct0700h100ml images!"
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"
#Waiting to Resume from Checkpoint "Release puck top pressure"
#"brent 7096"\Session Begun
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}]]></property>
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<property name="body"><![CDATA[Materials for Accel cartridge testing
# [Cartridge assembly document from Accel|^Cartage Assembly Procedure.docx|cartridge build procedure]\\


h2. +Test Plan v1&nbsp; (Sep 13, 2013)+

Must label ports/paths on cartridges

Convention for syringes (with spool valve on left) will be:
|| 0 || 1\\ || 2\\ || 3\\ || 4 \\ ||
| Spool valve\\ | check valve | check valve \\ | | |
| | spring | | | |
| | air | RNALater | waste | waste \\ |
\\ \\

h5.


h4. Filtration Speed and Evac
\--22 PSI thru puck within CARTRIDGEwithin Accel Test Holder

within G2 holderusing raw seawater, with x3 replica's
h4. Syringe Functions
\--How to load syringes

\--check valves; do they leak or hold pressure?

\-After Final Assembly Testing by hand:
\--define actuation process

\--build bench testing actuator
h4. Full Assembly sub-test&nbsp; (all testing will have companion G2 comparison test)

&nbsp;--filter

\--move spool valve

\--evac w/ push

\--remove puck and weigh

When procedure refined, run w/ 0.45 filter and filter 'stacks'
h4. Final Assembly Test (all testing will have companion G2 comparison test)
&nbsp;--filter

\--move spool valve

\--evac w/ push

\--hit with RNALater

\--remove and process filter ]]></property>
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<id name="id">10387497</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore)
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated and inconsistent format.  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketd by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}]]></property>
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</property>
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<id name="id">22544414</id>
<property name="body"><![CDATA[Materials for Accel cartridge testing
# [Cartridge assembly document from Accel|^Cartage Assembly Procedure.docx|cartridge build procedure]
# [Cartridge (v1) BOM|^BOM MBARI 2013-09-17 ARCHIVE CARTRIDGE.pdf|BOM]

h2. +Test Plan v1&nbsp; (Sep 13, 2013)+

Must label ports/paths on cartridges

Convention for syringes (with spool valve on left) will be:
|| 0 || 1 \\ || 2 \\ || 3 \\ || 4 \\ ||
| Spool valve \\ | check valve | check valve \\ | | |
| | spring | spring | | |
| | air | RNALater | waste | waste \\ |
\\
\\

h5.


h4. Filtration Speed and Evac

\--22 PSI thru puck within CARTRIDGEwithin Accel Test Holder

within G2 holderusing raw seawater, with x3 replica's

h4. Syringe Functions

\--How to load syringes

\--check valves; do they leak or hold pressure?

\-After Final Assembly Testing by hand:
\--define actuation process

\--build bench testing actuator

h4. Full Assembly sub-test&nbsp; (all testing will have companion G2 comparison test)

&nbsp;--filter

\--move spool valve

\--evac w/ push

\--remove puck and weigh

When procedure refined, run w/ 0.45 filter and filter 'stacks'

h4. Final Assembly Test (all testing will have companion G2 comparison test)

&nbsp;--filter

\--move spool valve

\--evac w/ push

\--hit with RNALater

\--remove and process filter [BOM MBARI 2013-09-17 ARCHIVE CARTRIDGE.pdf|^BOM MBARI 2013-09-17 ARCHIVE CARTRIDGE.pdf|Cartridge v1 BOM]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">22511646</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">22544413</id>
<property name="body"><![CDATA[Materials for Accel cartridge testing
# [Cartridge assembly document from Accel|^Cartage Assembly Procedure.docx|cartridge build procedure]
# [Cartridge (v1) BOM|^BOM MBARI 2013-09-17 ARCHIVE CARTRIDGE.pdf|BOM]

h2. +Test Plan v1&nbsp; (Sep 13, 2013)+

Must label ports/paths on cartridges

Convention for syringes (with spool valve on left) will be:
|| 0 || 1 \\ || 2 \\ || 3 \\ || 4 \\ ||
| Spool valve \\ | check valve | check valve \\ | | |
| | spring | | | |
| | air | RNALater | waste | waste \\ |
\\
\\

h5.


h4. Filtration Speed and Evac

\--22 PSI thru puck within CARTRIDGEwithin Accel Test Holder

within G2 holderusing raw seawater, with x3 replica's

h4. Syringe Functions

\--How to load syringes

\--check valves; do they leak or hold pressure?

\-After Final Assembly Testing by hand:
\--define actuation process

\--build bench testing actuator

h4. Full Assembly sub-test&nbsp; (all testing will have companion G2 comparison test)

&nbsp;--filter

\--move spool valve

\--evac w/ push

\--remove puck and weigh

When procedure refined, run w/ 0.45 filter and filter 'stacks'

h4. Final Assembly Test (all testing will have companion G2 comparison test)

&nbsp;--filter

\--move spool valve

\--evac w/ push

\--hit with RNALater

\--remove and process filter [BOM MBARI 2013-09-17 ARCHIVE CARTRIDGE.pdf|^BOM MBARI 2013-09-17 ARCHIVE CARTRIDGE.pdf|Cartridge v1 BOM]]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387493</id>
<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10354725</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">22544415</id>
<property name="body"><![CDATA[Materials for Accel cartridge testing
# [Cartridge assembly document from Accel|^Cartage Assembly Procedure.docx|cartridge build procedure]
# [Cartridge (v1) BOM|^BOM MBARI 2013-09-17.xlsx|BOM]

h2. +Test Plan v1&nbsp; (Sep 13, 2013)+

Must label ports/paths on cartridges

Convention for syringes (with spool valve on left) will be:
|| 0 || 1 \\ || 2 \\ || 3 \\ || 4 \\ ||
| Spool valve \\ | check valve | check valve \\ | | |
| | spring | spring | | |
| | air | RNALater | waste | waste \\ |
\\
\\

h5.


h4. Filtration Speed and Evac

\--22 PSI thru puck within CARTRIDGEwithin Accel Test Holder

within G2 holderusing raw seawater, with x3 replica's

h4. Syringe Functions

\--How to load syringes

\--check valves; do they leak or hold pressure?

\-After Final Assembly Testing by hand:
\--define actuation process

\--build bench testing actuator

h4. Full Assembly sub-test&nbsp; (all testing will have companion G2 comparison test)

&nbsp;--filter

\--move spool valve

\--evac w/ push

\--remove puck and weigh

When procedure refined, run w/ 0.45 filter and filter 'stacks'

h4. Final Assembly Test (all testing will have companion G2 comparison test)

&nbsp;--filter

\--move spool valve

\--evac w/ push

\--hit with RNALater

\--remove and process filter [BOM MBARI 2013-09-17 ARCHIVE CARTRIDGE.pdf|^BOM MBARI 2013-09-17 ARCHIVE CARTRIDGE.pdf|Cartridge v1 BOM]]]></property>
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<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore)
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated and inconsistent format.  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketd by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.]]></property>
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<id name="id">10387521</id>
<property name="body"><![CDATA[# [Comments from July 9, 2008 Design Review]
# [Doug's collected comments of 9 july CDR]

* [DWSM fluid Diagram]]]></property>
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</property>
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<id name="id">10387522</id>
<property name="body"><![CDATA[# [Comments from July 9, 2008 Design Review]
# [Doug's collected comments of 9 july CDR]

* [The DWSM scheme |^4k DWSM Operation.ppt]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10354755</id>
</property>
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<id name="id">10387519</id>
<property name="body"><![CDATA[April 6--Bruce at M0 for surface deployment

April 15--Mack in Sphere for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

April 29--Recover Bruce at M0

May 1--Mack in sphere connected to DWSM(dive #3); incredible success.&nbsp; Nat Geo filmed dive.]]></property>
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<id name="id">10387515</id>
<property name="body"><![CDATA[# [Comments from July 9, 2008 Design Review]
# [Doug's collected comments of 9 july CDR]

# [DWSM fluid Diagram]]]></property>
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<id name="id">10387513</id>
<property name="body"><![CDATA[Present: Wayne, Cheri, Gene, Kevin, Jim, Doug, Scott
Absent: Addie, Chris S.

h3.  Machine Builds
*  History:  At end of last surface deployment with Bruce, near end of mission, PS and PC started losing position and going in wrong direction.
** Upon recovery, Cheri ran several hundred PS/PC moves and the error never repeated.
** Yesterday NEO (deployed) showed exact same error.
** Cheri will check to see what bit version Bruce has (may not have the latest)
* Scott discovered dwarf/r-valve issue (1K resistor used instead of 100K);  Dwarfs in DWSM/D-ESP have already ben changed.  This is a problem in ALL ESP's, but unclear if it results in errors we see on Bruce and NEO.
* PC and CC springs on Bruce have been replaced.  Cheri noticed CC temp sensor needed replacement and is doing thermal calibration today.
* While temperature calibrating, will finish build of Gordon and Betty's hands.  Both should be installed by end of today.

h3. MFB

* PCR module #07 has arrived.

h3. Drifter

* 

h3. Software



h3. Deep ESP/DWSM

* Brent working on software.
* High Pressure test for leak in DWSM is tomorrow.  Doug working out how to tighten bells with minimum fuss.  Van will be cooled to 2C tonight, bells tightened tomorrow AM, and pressure raised to 3000psi at the intake port.  Minimum test is to see if anything leaks in upper bells.  may try and move valves


h3. GUI

* Will be loaded on Gordon and Betty for beta testing.

h3. Deployment Issues

For June:
* Mack in sphere
* Bruce in Drifter
* Moe on bench&nbsp;

\\
\\
\\

h3. &nbsp;Other Items:

* need loaner computer from IS for summer student&nbsp; (Cheri will put in request with IS for what we need)
Here is the schedule for the next two weeks:]]></property>
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<id name="id">10387514</id>
<property name="body"><![CDATA[# [Comments from July 9, 2008 Design Review]
# [Doug's collected comments of 9 july CDR]]]></property>
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<id name="id">10387511</id>
<property name="body"><![CDATA[h3. MFB


h3. Drifter

* Test tank tomorrow (Friday).
* Dive days moved to 27 and 28 next week. Likely will only use the 27th.
* There will be no tension control on winch for June dive.
* Pressure transducer and moxa need mounting on lid
** need fitting and adaptor using power port on lid
** Mike P to make bracket for MOXA
** Roman to move mooring to high bay; Jim to get Ken Smith batteries
* Gene wants ESP 100lbs negative.&nbsp; Will work with Mike to accomplish.
* BRUCE is going in drifter

h3. Software

* &nbsp;

h3. Deep ESP


h6.

* Wand; don't have cables long enough for long wand assembly.&nbsp; Cables arrive 29th (too late)
* Will shoot for a 3' stubby.&nbsp; Code still to be developed
* TSV--needed tightening
* CPLD code works but needs testing
* Mink is soldered and waiting for modem before potting.
* D-ESP cleaning
** Doug has two 4" sections that can't be cleaned with toxicant.&nbsp; So idea is to add a filter puck taht we push tox through the core to clean both those lines in DWSM, then go to next SH1 run.

h3. GUI

* Will be loaded on Gordon and Betty for beta testing.

h3. Deployment Issues

For June:
* Mack in sphere
* Bruce in Drifter
* Moe on bench&nbsp;

\\
\\
\\

h3. &nbsp;Other Items:

* need loaner computer from IS for summer student&nbsp; (Cheri will put in request with IS for what we need)
Here is the schedule for the next two weeks:]]></property>
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<id name="id">10387508</id>
<property name="body"><![CDATA[This page is intended to provide just enough information about the ESP's raw file format so that the ESP GUI can parse it to extract time and data management entries.  More complete documentation is available in MBARI's CVS repository in the file:  ESP/gen2/software/esp/lib/log.rb.

The raw, real-time log is typically named *real.log*.  The actual log file name is determined by the mode of ESP operation that generated it.  A quick simulation log of a mission would be written to *quick.log*, for example.  A real-time simulation would be written to *simreal.log*
\\

All raw log files consist of a series of log entries, each of which is separated by a single ASCII linefeed (0x0a) character.  Each log entry line begins with a byte that denotes its type.  This simple record structure allows one to easily skip over types of log entries they do not recognize. The types of log entries that the GUI will probably want to process are _timestamp,_ _time_mark,_{_}time_increment,_ _alias_definition_ and _gui_data_ records. These log enties conform to the following grammar:
\\
\\

*Non-terminals:* (terminal symbols enclosed in <>)

digit = <0>..<9>

capital = <A>..<Z>

alpha = capital \| <a>..<z>

timezone = capital\[capital\]?\[capital\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #Ex.&nbsp; GMT, PST, PDT, Z

moniker = alpha\|digit

character = <any byte except <">, <\>, <linefeed>> \| <\><"> \| <\><\> \| <\><linefeed>

string = \[character\]\+

actor = <">string<">\|moniker\|<\>
\\
\\

*Log entries:*

time_mark = <@>digit*\[<.>digit+\]?timezone	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3.14PST, .1PST, 999.01GMT, 1232498793.34PST

timestamp = <@>timezone?digit*\[<.>digit+\]?\[</>digit*\[<.>digit+\]?\]? &nbsp;&nbsp; #Ex.&nbsp; 3.14, .1, 999.01, PST1232498793.34/100.0

time_increment = <+>digit\*		 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #Ex.&nbsp; 3, 0, 100

alias = <=>moniker?\[<">string<">\]?	 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; #Ex.&nbsp; =tMAIN, =hcore, =ECan

gui_data = <`>actor?string		&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; #not context free, see notes below
\\
\\

*Grammar Notes:*

The actor non-terminal token in the gui_data production may be omitted if the first character of the following string is not equal to any moniker defined in a previous alias_definition.  Otherwise, the&nbsp; placeholder actor <\> must be inserted before the string.

An alias without a "string" deletes the alias associated with the indicated moniker

A alias missing moniker (and "string") deletes all aliases.

time_increment with no digits <+> is equivalent to \+1 tic.
\\
\\

*Example raw gui_data log entries:*

`arbitrary text

`"thread_name"arbitrary text      	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #switched to thread_name

`\Sam is cool			 	&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; #There is an actor whose moniker is 'S', so it must be escaped

`\Saturday symphony \

on the lawn \

in the park.				&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; #multiline text
\\
\\

*Tracking Log Time:*

_timestamps:_&nbsp; Set the current log time.
* If the timezone is specified, system is operating in real-time.
* Real log time is Epoch seconds from Midnight 1/1/70 GMT.
* If the timezone is omitted, system is operating in simulated time
* Simulated log time is simply (simulated) seconds from simulation start.
* Assume 100 Tics Per Second if tics per second is omitted

_time_increments_:&nbsp; Increment the current real or simulated log time by specified number of tics.
\\

_time_marks:_ Indicate the Real-time at which the entry was generated.
* The timezone is always specified.
* Does not alter the current log time.

Each log entry has a "context" that consists of its log time and the actor that wrote it.
\\

*Initialize log entry context upon raw log file open:*

logTime = 0

timeZone=:simulated

actors = {}   #empty hash

actor = ""

ticsPerSecond = 100&nbsp;&nbsp;&nbsp; #default tics per second
\\

*GetNextGuiDataText:*
\\

loop do

&nbsp;&nbsp;&nbsp; case (entry type)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; when timestamp:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime = epoch seconds specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; if (zone specified)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; timeZone=zone from timestamp

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  if (ticsPerSecond specified)
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  ticsPerSecond = ticsPerSecond from timestamp&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when time_increment:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if increment specified

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; logTime \+= specified increment / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;&nbsp;  logTime \+= 1 / ticsPerSecond

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp; round logTime to the nearest tic&nbsp;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when alias:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp; if (moniker present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (string present)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; actors\[moniker\] = string

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; actors.delete moniker

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;  &nbsp;&nbsp;  else

&nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  &nbsp;&nbsp;  actors.clear&nbsp; #delete all monikers from hash

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; continue;

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; when gui_data:

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; c = character following <`>

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; if (c == <"> )

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = text between quotes

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if (c == <\>)

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else if moniker\[c\] exists

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; actor = moniker\[c\]

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return  next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; else

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; return c + next character to end of entry

&nbsp;&nbsp;&nbsp; &nbsp; end&nbsp; #case

end&nbsp; #loop

h3. Parsing Rules

Given the above information, here are the rules that will be applied to parsing a raw log file (.log):

# Comments will be key lines to utilize in the parsing. Email ones are particularly important as they will correspond to emails sent to users (they will be able to make links intuitively). (i.e. Comments generated by the code can't be changed nilly-willy anymore).  The goal with the GUI log entries is to eliminate the reliance of the GUI on the comments and to have log entries that will be less likely to change in the code base.
# A line generated by the "Qmail" actor that contains the phrase "GoodNews.email "Starting w/pucks" indicates the staring of a mission that is driven by a mission script.
# A comment with that matches the pattern "XXXX sampling at most YYYY.Yml" indicates that an assay with the name "XXXX" is starting and will attempt to draw a water sample of YYYY.Yml.
## These lines can have multiple assays that are comma separated (the first entry has the phrase 'sampling' the subsequent ones do not).  Here is an example:
{noformat}
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}
indicates that an assay named 'hab' will run and will attempt to draw a 100.0ml water sample.  That will then be followed by an assay named 'wcr' that will attempt to draw 50.0ml.
# Samples can be bracketed by two comments:
## Start sample is indicated by a comment of form "Sampling XXX.Xml"
## End sample is indicated by a comment of form "Sampled XXX.Xml" where the XXX.Xml indicates that actual amount of water sampled.
{note:title=Link to assay}
Note that these parsed samples will be linked to the list of assays that was indicated by the "XXXX sampling at most YYYY.Yml" lines.  In other words, if there are two comma separated assays in this line, there should be two samples bracketd by "Sampling" and "Sampled" and should be in the order indicated by the "sampling at most" log entry.
{note}
# ESP Can data is combined with ancillary instrument data in a single log entry that is separated by new lines.  An example:
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W
CTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V
ISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
{noformat}

h3. Important log entries
{noformat}
#\Can@16:58:49, 21.5C, 20% humidity, 14.5psia, 15.267V, 0.561A, 0.561A avg, 8.56W\\nCTD@17:03:25, 19.2905C, 0.008 decibars, 0.0000 S/m, 1.94 mg/m^3, 3.8176V\\nISUS@17:03:49, 5.250 uM/L no^3, -1.000 uM/L hs, 0.0100 psu
."Qmail"GoodNews.email "Starting w/pucks in tube 2\\nEnding Tue Oct 07 06:00:00 PDT 2008",:Subject=>"08oct06mack begun"
."Qmail"GoodNews.email "Then, in tube 2:  initialPurge; habda [1000.0,50.0]\\n/home/esp/esp2/mission/08oct08mack.rb:13",:Subject=>"Asleep until 18:00 PDT 11-Oct-08"
."Qmail"HABfans.email "Can@22:44:45, 22.0C, 12% humidity, 14.8psia, 15.744V, 0.384A, 0.390A avg, 6.04W\\nCTD@22:45:23, 22.0495C, 0.010 decibars, 0.0000 S/m, -1.58 mg/m^3, 94.76%, 0.215 1/m\\nISUS@22:45:46, 12.350 uM/L no^3, -1.000 uM/L hs, 32.5700 psu",:Subject=>"hab sampling at most 100.0ml, wcr at most 50.0ml"
#"sh2"\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
#\PuckCamera: snap -bin=2,2 40 /var/log/esp/hab08oct0700h100ml40s.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
#\PuckCamera: snap -bin=2,2 -auto /var/log/esp/midres/hab08oct0700h100ml.tif
#\Starlight Xpress HX9/16: 1392x1040 pixel 16-bit CCD camera
."Qmail"HABfans.email "56.113 sec auto-exposure",:Subject=>"hab08oct0700h100ml images!"
."Qmail"GoodNews.email "Asleep logging context until 06:00",:Subject=>"mack completed 08oct06mack assays"
."Qmail"BadNews.email "Processing Syringe speedErr",:Subject=>"Slide::Error in sh2"
."Qmail"BadNews.email "Hand could not finish releasing because\\nNo Response to I2C::Servo::ReleaseRequest[10:->26]",:Subject=>"I2C::Request::Timeout in MAIN"
."Qmail"BadNews.email "undefined method `axis' for \\#<I2C::Request::Timeout:0x2afcbf70>",:Subject=>"NameError in MAIN"
."Qmail"BadNews.email "Collection Syringe aborted",:Subject=>"Slide::Error in readyCS"
."Qmail"BadNews.email "Sampler Syringe aborted",:Subject=>"Slide::Error in rdySampler"
."Qmail"BadNews.email "Processing Syringe aborted",:Subject=>"Slide::Error in rdyProcessing"

#Waiting to Resume from Checkpoint "Heating sh1 puck from tube 2 in Collection Clamp to 85.0C for 5:00"
."Qmail"BadNews.email "Collection Puck Heater could not reach 85.0C in 8:00",:Subject=>"Thermal::Error in MAIN"

#"brent 7096"\Session Begun
#t\hab sampling at most 100.0ml, wcr at most 50.0ml
{noformat}]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387653</id>
<property name="body"><![CDATA[h3. +These are deployments arranged Chronologically during 2009+


April 6--Bruce at M0 for surface deployment

April 15--Mack in Sphere for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

April 29--Recover Bruce at M0

May 1--Mack in sphere connected to DWSM(dive #3); incredible success.&nbsp; Nat Geo filmed dive.

May 14--Deploy NEO w/PCR, surface deployment

May 27--First Drifter dive (Zephyr)

June 5-9 \-\- Western Flyer.&nbsp; D-ESP, Drifter, and CTD casts. ]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10354889</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387654</id>
<property name="body"><![CDATA[h3. +These are deployments arranged Chronologically during 2009+

April 6--Bruce at M0 for surface deployment (Zephyr)


April 15--Mack in Sphere for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

April 29--Recover Bruce at M0 (Zephyr)


May 1--Mack in sphere connected to DWSM(dive #3); incredible success.&nbsp; Nat Geo filmed dive. (Lobos)


May 14--Deploy NEO w/PCR, surface deployment (Zephyr)


May 27--First Drifter dive (Zephyr)

June 5-9 \-\- Western Flyer.&nbsp; D-ESP, Drifter, and CTD casts.

June 11 \-\- Recover NEO.&nbsp; (Zephyr) ]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387616</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Surface Can (plans)]
# [4K Sphere|Shallow Housing Portfolio4.pdf]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10354852</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387615</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Surface Can (plans)]
# [4K Sphere|ESPAPP:ESP -- SURF Center Main Page^Shallow Housing Portfolio4.pdf?]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10354850</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387618</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Surface Can (plans)]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10354854</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387612</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# Surface Can (plans)
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10354846</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387611</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10354845</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387613</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Surface Can (plans)]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10354848</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387621</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Surface Can (plans)#Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10354857</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387619</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Surface Can (plans)#ESPAPP:ESP -- SURF Center Main Page^Shallow Housing Portfolio4.pdf?]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10354855</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387632</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow%Housing%Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387629</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Surface Can (plans)^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10354865</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387630</id>
<property name="body"><![CDATA[h1. Welcome to the ESP - SURF Center project\!


h3. Administrative

# [2007 Meeting Notes]
# [2008 Meeting Notes]
# [2009 Meeting Notes]

h2. Engineering


h4. System Integration

# [System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]
# [Engineering Timeline] 2008
# [Cheat Sheet]
# [Container Storage Locker Information (10-1-2008)]

h4. Hardware

# [Micro-Fluidics Block]
# [LLNL PCR heater module]
# [Shallow Housing Plans|^Shallow Housing Portfolio4.pdf]
# [4K Sphere]
# [DWSM--4k Deep Water Sampling Module]
# [Puck Numbering System]
# [Frit Identification system]

h4. Software

# [JIRA Bug Tracker|https://oceana.mbari.org/jira]
# [GUI Component Development Pages|2G ESP GUI Project Page]
# [ESP Image Analysis Application]
# [Power Commands (9-30-08)]
# [Radio Communication commands for tri-deployment (10-7-08)]
# [Software Cheat Sheet|ESPAPP:Cheat Sheet|A software cheat sheet]
# [How To Get the ESP Software Running On Your Machine]

h2. Science

# [2008 Deployments]
# [2009 Deployments]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10354866</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">27099210</id>
<property name="body"><![CDATA[h4. {color:#ff00cc}SCCWRP--San Diego{color}

Originally to begin Jan 14, 2014, but SCCWRP did/could not install pier pump.&nbsp; Sampling began?? and ended ~ week later when pump tore from piling.

*March 5, 2014*

ESP-NEO w/ MFB10. Running WCR and water quality PCR probes
Located at [Ocean Pier|^SCCWRP_OceanBeach_Recon-2.docx|Recon document] (extension of Niagara Ave, San Diego).
Original schedule is [here|^2014_ESP_SCCWRP_Cal(original).doc|This was our dream...].

*Sept 25*

ESP-NEO returned after being stored in (un-airconditioned) shed, unopened since above date.&nbsp; Bleach had leaked and corroded all internal components.


h4. {color:#ff00cc}Catalina Island--Moore Applications-Jed Fuhrman{color}

*March 18, 2014*

ESP-Moe, no PCR.  Mostly WCR with some BAC arrays
Mooring details [here|^Catalina2014MooringConfigurationREV2.pdf|Catalina mooring measurments].

MELO used was #300034012090780

location reported by MELO was-\- &nbsp; 33.4865 \-118.51285

*March 20*\--lost comms

*March 21*\--re-established comms and think problem in E/M cable.

*March 22*\--lost comms

*April 3*\--small boat to buoy to test E/M cable

*April 8*\--'rescue' mission. Swapped E/M cables and repositioned in slightly deeper water, at 33.48504 \-118.50988

water depth 175m.&nbsp; top of can 10.9m

*RECOVERY--see below*

h4. {color:#ff00cc}ECOHAB--S. California{color}

*April 1*\--Instruments deployed

&nbsp;MOE--inshore at 33.60779 \-118.01877 with ISUS

Melo was 300234060014550

avg can depth \~9m
\\

&nbsp;Bruce--offshore at 33.58609 \-118.03686

Melo was 300234060016190

avg can depth \~19.5m

*~ April 9* lost communication with Bruce.&nbsp;

*April 15*\--Rescue mission w/Nerissa found 'hung' modem.&nbsp; Power cycled and checked cables on deck.&nbsp; Re-deployed in nearby spot.&nbsp; Divers (Kim R. & George M) measured 17.7m to top of can, 25.3 m to master link.

*RECOVERY*\--Plan was to pull ECOHAB April 30 with LBA0P divers off Nerissa, Catalina with Wrigley divers off Yellowfin May 1.&nbsp;&nbsp; April 30 had horrible Santa Ana winds; motored offshore to Bruce, and too rough.&nbsp; Cancelled entire day.&nbsp; Would try next day as winds supposed to die.&nbsp; Met at 5am and decided to cancel again, as winds were still blowing.&nbsp; Drove to Long Beach, and no wind up there. Salvaged that day by rounding up crew and wrigley divers after initially cancelling and heading over about noon.&nbsp; During that time, Dennis (skipper of Yellowfin) agreed to go the next day (Friday) to retrieve the two ECOHAB instruments.&nbsp; Eric Reinecker came down from MBARI, joining Jim Citanovich from SCMI and we retrieved Mack and Bruce.&nbsp; Back at SCMI around 1pm.&nbsp; Flatbed loaded by 4:30.&nbsp; Returned to MBARI next day (Saturday).

h4. {color:#ff00cc}Sulfur Cycling (Moran)--Monterey Bay{color}

*Sep 15*\--Instrument deployed

&nbsp;ESP-Gordon--at 36.83113 \-121.91114&nbsp; (M0) with ISUS and CTD.&nbsp; Forgot to start Melo (did it next day).&nbsp; Running archive-only mission, ended up deeper than we had hoped (~12m instead of 7-10m).

Sep 18--Went out in Paragon w/ 2 divers (Eric R & Lisa Z.).&nbsp; Pulled \~0.5mi toward M0.&nbsp; Now at 36.83480 \-121.89800 at 5-8m.&nbsp; Sampling has resumed. ]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# Clean minimal install of CentOS 7

h3. Steps to build and run

# I had to install the development tools group as well using:
{code}
sudo yum groupinstall "Development Tools"
{code}
# Next, make sure 'git' is installed.
{code}
sudo yum install git
{code}
# Next, you need to install the MBARI custom ruby environment.  This can be checked out of Brent Roman's Github repo by using:
{code}
git clone https://github.com/brentr/matzruby.git
{code}
which created a matzruby directory in my home directory
# I then cd'd into the matzruby directory and ran
{code}
git checkout esp
{code}
# Then I changed the espconfig and configure files to executable using
{code}
chmod a+x espconfig
chomd a+x configure
{code}
# I had to edit the espconfig file and put a './' in front of the two 'configure' entries in the file
# Then I ran
{code}
./espconfig
{code}
# Followed by
{code}
./espinstall
{code}
which seemed to work and install ruby executable in /opt/mbari/bin/ruby
# In my home directory, I created an 'esp' subdirectory and cd'd into it.
# I then checked out the ESP code from the Git rep using:
{code}
git clone https://github.com/MBARI-ESP/ESP2Gscript.git
{code}
which creates a "ESP2Gscript" directory
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/esp/ESP2Gscript
export ESPname=neo
export ESPmode=simfast
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin:/opt/mbari/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# Then you cd'd to a directory where there are mission scripts(i.e. mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# Clean minimal install of CentOS 7
# Git client

h3. Steps to build and run

{noformat}
# I first installed wget so I could pull down an older version of GCC.  I did this using yum:
{code}
sudo yum install wget
{code}
# Then I installed bzip2 (which is needed later) using:
{code}
sudo yum install bzip2
{code}
{noformat}
# I had to install the development tools group as well using:
{code}
sudo yum groupinstall "Development Tools"
{code}
{noformat}
# I had to install the libc devel package too
{code}
sudo yum install glibc-devel.i686
{code}
# This installs the latest gcc, but we need version 4.6.3 installed, so I downloaded the source tar using:
{code}
wget http://ftp.gnu.org/gnu/gcc/gcc-4.6.3/gcc-4.6.3.tar.gz
{code}
# I then unzipped the download using:
{code}
gunzip gcc-4.6.3.tar.gz
{code}
# I un-tarred the file using:
{code}
tar -xvf gnu-4.6.3.tar
{code}
which created a gcc-4.6.3 directory
# I cd'd into that directory and ran
{code}
./contrib/download_prerequisites
{code}
# Once that finished, I built the gcc compiler using:
{code}
./configure --prefix=/usr/local/gcc/4.6.3
{code}
# Then run:
{code}
make
{code}
# And finally, install using:
{code}
sudo make install
{code}
{noformat}
# Next, make sure 'git' is installed.
{code}
sudo yum install git
{code}
# Next, you need to install the MBARI custom ruby environment.  This can be checked out of Brent Roman's Github repo by using:
{code}
git clone https://github.com/brentr/matzruby.git
{code}
which created a matzruby directory in my home directory
# I then cd'd into the matzruby directory and ran
{code}
git checkout esp
{code}
# Then I changed the espconfig and configure files to executable using
{code}
chmod a+x espconfig
chomd a+x configure
{code}
# I had to edit the espconfig file and put a './' in front of the two 'configure' entries in the file
# Then I ran
{code}
./espconfig
{code}
# Followed by
{code}
./espinstall
{code}
which seemed to work and install ruby executable in /opt/mbari/bin/ruby
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/esp/ESP2Gscript
export ESPname=neo
export ESPmode=simfast
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin:/opt/mbari/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# In my home directory, I created an 'esp' subdirectory and cd'd into it.
# I then checked out the ESP code from the Git rep using:
{code}
git clone https://github.com/MBARI-ESP/ESP2Gscript.git
{code}
which creates a "ESP2Gscript" directory
# by copying the *.rb files (about 4) from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/_version_
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# Clean install of CentOS 6.6 (this has gcc 4.4 by default)

h3. Steps to build and run

# I first logged in as kgomes
# Then opened a terminal window
# I changed to root using
{code}
su
{code}
# I then created the log directory by doing
{code}
cd /var/log
mkdir kgomes
chown kgomes:kgomes kgomes
{code}
# I made sure git was installed.  It was not so I installed it using
{code}
yum install git
{code}
# I also had to install autoconf using
{code}
yum install autoconf
{code}
# And I had to install yacc using
{code}
yum install byacc
{code}
# Then I changed to the root home directory using
{code}
cd
{code}
# I created a directory I could work in using
{code}
mkdir esp
{code}
# Changed into that directory using
{code}
cd esp
{code}
# I needed to build the MBARI version of Ruby, so I checked it out from Brent's repo using
{code}
git clone https://github.com/brentr/matzruby.git
{code}
# That created a matzruby directory which I then changed into using
{code}
cd matzruby
{code}
# Not sure why, but running ./espconfig did not work due to some path problems so to fix this, I edited the espconfig file and adding './' in front of 'configure' in two places
# Then I was able to run espconfig this way
{code}
./espconfig
{code}
# Once that completed, I ran
{code}
./espinstall
{code}
which installed the ruby executable in /opt/mbari/bin
# I then exited out of the root shell
{code}
exit
{code}
which put me back in my kgomes account
# I created a working directory by using
{code}
mkdir esp
{code}
# Changed into it using
{code}
cd esp
{code}
# I tried to clone the repository, but kept getting a 403 (unauthorized) error which I am sure had something to do with my git configuration as it would not ask for my username and password event though this is a private rep.  To get around this, I just opened a browser, logged into to github and downloaded the zip file which I put in the esp directory.
# Now, in order to setup the ESP environment so it can run on my machine, I edited my .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/esp/ESP2Gscript-master
export ESPname=gordon
export ESPmode=simreal
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin:/opt/mbari/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# Once this was done, I was successfully able to run
{code}
esp
{code}
to get the ESP server running]]></property>
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## [ESP Configuration In Lab]
## [ESP Deployment]
## [ESP Operations]
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Archived Documentation}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]

# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.

Now you can run through the [ESP GUI Users Guide]
{panel}
]]></property>
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## [ESP Configuration In Lab]
## [ESP Deployment]
## [ESP Operations]
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]

The original ESP GUI was a Java application that was connected to a SQL database.  Here are the use instructions for that application (some links don't work).
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.

Here is the original [ESP GUI Users Guide] for the Java application
{panel}
]]></property>
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## [ESP Configuration In Lab]
## [ESP Deployment]
## [ESP Operations]
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.

Now you can run through the [ESP GUI Users Guide]
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
{panel}
{column}
{column:width=50%}

{column}
{section}


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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## [ESP Configuration In Lab]
## [ESP Deployment]
## [ESP Operations]
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Archived Documentation}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.

Now you can run through the [ESP GUI Users Guide]
{panel}
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## [ESP Configuration In Lab]
## [ESP Deployment]
## [ESP Operations]
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [ESP Java GUI]
# Original [ESP GUI Users Guide]
{panel}
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# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## [ESP Configuration In Lab]
## [ESP Deployment]
## [ESP Operations]
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [Original Java GUI Application|]
Here is the original [ESP GUI Users Guide] for the Java application
{panel}
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## [ESP Configuration In Lab]
## [ESP Deployment]
## [ESP Operations]
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]

The original ESP GUI was a Java application that was connected to a SQL database.  Here are the use instructions for that application (some links don't work).
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.

Here is the original [ESP GUI Users Guide] for the Java application
{panel}
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# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.

Now you can run through the [ESP GUI Users Guide]
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# Use Cases
## [ESP Configuration In Lab]
## [ESP Deployment]
## [ESP Operations]
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking (JIRA)|https://oceana.mbari.org/jira/browse/ESPII]
{panel}
{column}
{section}


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<property name="body"><![CDATA[{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.

Now you can run through the [ESP GUI Users Guide]
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# Use Cases
## [ESP Configuration In Lab]
## [ESP Deployment]
## [ESP Operations]
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{column}
{section}


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<property name="body"><![CDATA[h5. Current Application(s)

# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# Use Cases
## [ESP Configuration In Lab]
## [ESP Deployment]
## [ESP Operations]
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.

Now you can run through the [ESP GUI Users Guide]
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}

{column}
{section}


]]></property>
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# Use Cases
## [ESP Configuration In Lab]
## [ESP Deployment]
## [ESP Operations]
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.

Now you can run through the [ESP GUI Users Guide]
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}

{column}
{section}


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<property name="body"><![CDATA[h5. Current Application(s)

{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.

Now you can run through the [ESP GUI Users Guide]
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# Use Cases
## [ESP Configuration In Lab]
## [ESP Deployment]
## [ESP Operations]
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{column}
{section}


]]></property>
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<property name="body"><![CDATA[h5. Current Application(s)

# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]

{panel:title=Current Version of the Application|titleBGColor=#5ed0ff|borderWidth=5}
# _MBARI Central DB_: Use this one if you want to run the GUI against the central MBARI database hosted on a Microsoft SQL Server.
## Launch using [JNLP|http://ssdsmac.shore.mbari.org/esp-gui/launch.jnlp]
## Download the [GUI Application|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar] and launch by:
### Command line: 'java -jar esp-gui-0.2-SNAPSHOT-jar-with-dependencies.jar'
### Or you should be able to double click on the jar in most cases.
# _Localhost_: Download this version if you want to run the GUI and have it point to a local installation of a MySQL database
## Download the [localhost version|http://ssdsmac.shore.mbari.org/esp-gui/esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar] of the application
## If you have not setup the mysql database before, you will need to use the command line mysql client to create the database, user and assign permissions.  Do the following as root on a local installation of mysql
{noformat}
takoda:~ kgomes$ mysql --user=root --password=
Enter password:
mysql> CREATE DATABASE esp;
mysql> CREATE USER 'espdba'@'localhost' IDENTIFIED BY 'leghorn';
mysql> GRANT ALL PRIVILEGES ON esp.* TO 'espdba'@'localhost' WITH GRANT OPTION;
mysql> quit
{noformat}
## Launch the application either by command line with
{noformat}
java -jar esp-gui-0.2-SNAPSHOT-localhost-jar-with-dependencies.jar
{noformat}
or you should be able to double click on the jar in most cases.

Now you can run through the [ESP GUI Users Guide]
{panel}
{section}
{column:width=50%}
{panel:title=Project Information}
For the ESP Development projects, the proposals that are related to the GUI application development can be found here:
# [2007 project proposal|https://mww.mbari.org/resources/2007_Proposal_Process/phase_I_pdfs/900612_ESP_SURF_2007.pdf]
# [2008 project proposal|https://mww.mbari.org/resources/2008_Proposal_Process/phase_I_pdfs/900612_SURF_2008_Ph1_final.pdf]
# [2009 project proposal|https://mww.mbari.org/resources/2009_Proposal_Process/phase_I_pdfs/900915_SURF_2009_phase1_final.pdf]
# [2010 project proposal|https://mww.mbari.org/resources/2010_Proposal_Process/phase_I_pdfs/900915_SURF%20Center_2010_phase%201.pdf]
# [2011 project proposal|https://mww.mbari.org/resources/2011_Proposal_Process/phase_I_pdfs/900915_ESP_SURF_Center.pdf]
{panel}
{panel:title=Goals for GUI Application|width=60%}
The goals for the ESP GUI Application are:
# A graphical interface to allow the user to plan a mission for the ESP
# The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
# The GUI will provide functionality to manage the data from the ESP.  This data consists of:
## Various Ruby scripts
## Image analysis of the probe arrays
## Ancillary instrument data
## Events and data from log file (parsing)
# The GUI will provide a visual representation of the state of the ESP
## Currently user has to look through log file and mentally visualize state of system
## GUI should display visual representation of the instrument and its components
## Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
## The state visualization should be able to playback a mission run from a log file and step the user through instrument states
# The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
{panel}
{column}
{column:width=50%}
{panel:title=User Documentation}
{panel}
{panel:title=Design Documentation}
# Use Cases
## [ESP Configuration In Lab]
## [ESP Deployment]
## [ESP Operations]
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{column}
{section}


]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]]]></property>
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<id name="id">10387743</id>
<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically+


April 6--Bruce at M0 for surface deployment (Zephyr)

April 15--Mack in Sphere for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

April 29--Recover Bruce at M0 (Zephyr)

May 1--Mack in sphere connected to DWSM(dive #3); incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

May 14--Deploy NEO w/PCR, surface deployment (Zephyr)

May 27--First Drifter dive (Zephyr)

June 5-9 \-\- Western Flyer.&nbsp; D-ESP, Drifter, and CTD casts.

June 11 \-\- Recover NEO.&nbsp; (Zephyr) ]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# Clean minimal install of CentOS 7
# Git client

h3. Steps to build and run

# First, you need to install the MBARI custom ruby environment
# Next, make sure 'git' is installed.
{code}
sudo yum install git
{code}
# In my home directory, I created an 'esp' subdirectory and cd'd into it.
# I then checked out the ESP code from the Git rep using:
{code}
git clone https://github.com/MBARI-ESP/ESP2Gscript.git
{code}
which creates a "ESP2Gscript" directory
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/esp/ESP2Gscript
export ESPname=neo
export ESPmode=simfast
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# by copying the *.rb files (about 4) from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/_version_
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# Clean minimal install of CentOS 7
# Git client

h3. Steps to build and run

# I first installed wget so I could pull down an older version of GCC.  I did this using yum:
{code}
sudo yum install wget
{code}
# Then I installed bzip2 (which is needed later) using:
{code}
sudo yum install bzip2
{code}
# I needed to make sure I had gcc version 4.6.3 installed, so I downloaded the source tar using:
{code}
wget http://ftp.gnu.org/gnu/gcc/gcc-4.6.3/gcc-4.6.3.tar.gz
{code}
# I then unzipped the download using:
{code}
gunzip gcc-4.6.3.tar.gz
{code}
# I un-tarred the file using:
{code}
tar -xvf gnu-4.6.3.tar
{code}
which created a gcc-4.6.3 directory
# I cd'd into that directory and ran
{code}
./contrib/download_prerequisites
{code}
# Make sure you have gcc version 4.6 installed.  I did this by running:
{code}
sudo yum install gcc-4.6
{code}
# First, you need to install the MBARI custom ruby environment.  This can be checked out of Brent Roman's Github repo by using:
{code}
git clone https://github.com/brentr/matzruby.git
{code}
which created a matzruby directory in my home directory
# Next, make sure 'git' is installed.
{code}
sudo yum install git
{code}
# In my home directory, I created an 'esp' subdirectory and cd'd into it.
# I then checked out the ESP code from the Git rep using:
{code}
git clone https://github.com/MBARI-ESP/ESP2Gscript.git
{code}
which creates a "ESP2Gscript" directory
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/esp/ESP2Gscript
export ESPname=neo
export ESPmode=simfast
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# by copying the *.rb files (about 4) from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/_version_
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# Clean minimal install of CentOS 7
# Git client

h3. Steps to build and run

# I first installed wget so I could pull down an older version of GCC.  I did this using yum:
{code}
sudo yum install wget
{code}
# Then I installed bzip2 (which is needed later) using:
{code}
sudo yum install bzip2
{code}
# I needed to make sure I had gcc version 4.6.3 installed, so I downloaded the source tar using:
{code}
wget http://ftp.gnu.org/gnu/gcc/gcc-4.6.3/gcc-4.6.3.tar.gz
{code}
# I then unzipped the download using:
{code}
gunzip gcc-4.6.3.tar.gz
{code}
# I un-tarred the file using:
{code}
tar -xvf gnu-4.6.3.tar
{code}
which created a gcc-4.6.3 directory
# I cd'd into that directory and ran
{code}
./contrib/download_prerequisites
{code}
# Once that finished, I built the gcc compiler using:
{code}
./configure --prefix=/usr/local/gcc/4.6.3
{code}
# Next, you need to install the MBARI custom ruby environment.  This can be checked out of Brent Roman's Github repo by using:
{code}
git clone https://github.com/brentr/matzruby.git
{code}
which created a matzruby directory in my home directory
# Next, make sure 'git' is installed.
{code}
sudo yum install git
{code}
# In my home directory, I created an 'esp' subdirectory and cd'd into it.
# I then checked out the ESP code from the Git rep using:
{code}
git clone https://github.com/MBARI-ESP/ESP2Gscript.git
{code}
which creates a "ESP2Gscript" directory
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/esp/ESP2Gscript
export ESPname=neo
export ESPmode=simfast
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# by copying the *.rb files (about 4) from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/_version_
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">27066423</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">27099194</id>
<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# Clean minimal install of CentOS 7
# Git client

h3. Steps to build and run

# I first installed wget so I could pull down an older version of GCC.  I did this using yum:
{code}
sudo yum install wget
{code}
# Then I installed bzip2 (which is needed later) using:
{code}
sudo yum install bzip2
{code}
# I had to install the development tools group as well using:
{code}
sudo yum groupinstall "Development Tools"
{code}
# This installs the latest gcc, but we need version 4.6.3 installed, so I downloaded the source tar using:
{code}
wget http://ftp.gnu.org/gnu/gcc/gcc-4.6.3/gcc-4.6.3.tar.gz
{code}
# I then unzipped the download using:
{code}
gunzip gcc-4.6.3.tar.gz
{code}
# I un-tarred the file using:
{code}
tar -xvf gnu-4.6.3.tar
{code}
which created a gcc-4.6.3 directory
# I cd'd into that directory and ran
{code}
./contrib/download_prerequisites
{code}
# Once that finished, I built the gcc compiler using:
{code}
./configure --prefix=/usr/local/gcc/4.6.3
{code}
# Then run:
{code}
make
{code}
# And finally, install using:
{code}
sudo make install
{code}
# Next, you need to install the MBARI custom ruby environment.  This can be checked out of Brent Roman's Github repo by using:
{code}
git clone https://github.com/brentr/matzruby.git
{code}
which created a matzruby directory in my home directory
# Next, make sure 'git' is installed.
{code}
sudo yum install git
{code}
# In my home directory, I created an 'esp' subdirectory and cd'd into it.
# I then checked out the ESP code from the Git rep using:
{code}
git clone https://github.com/MBARI-ESP/ESP2Gscript.git
{code}
which creates a "ESP2Gscript" directory
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/esp/ESP2Gscript
export ESPname=neo
export ESPmode=simfast
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# by copying the *.rb files (about 4) from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/_version_
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">27066426</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">27099193</id>
<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# Clean minimal install of CentOS 7
# Git client

h3. Steps to build and run

# I first installed wget so I could pull down an older version of GCC.  I did this using yum:
{code}
sudo yum install wget
{code}
# Then I installed bzip2 (which is needed later) using:
{code}
sudo yum install bzip2
{code}
# I had to install the development tools group as well using:
{code}
sudo yum groupinstall "Development Tools"
{code}
# I needed to make sure I had gcc version 4.6.3 installed, so I downloaded the source tar using:
{code}
wget http://ftp.gnu.org/gnu/gcc/gcc-4.6.3/gcc-4.6.3.tar.gz
{code}
# I then unzipped the download using:
{code}
gunzip gcc-4.6.3.tar.gz
{code}
# I un-tarred the file using:
{code}
tar -xvf gnu-4.6.3.tar
{code}
which created a gcc-4.6.3 directory
# I cd'd into that directory and ran
{code}
./contrib/download_prerequisites
{code}
# Once that finished, I built the gcc compiler using:
{code}
./configure --prefix=/usr/local/gcc/4.6.3
{code}
# Next, you need to install the MBARI custom ruby environment.  This can be checked out of Brent Roman's Github repo by using:
{code}
git clone https://github.com/brentr/matzruby.git
{code}
which created a matzruby directory in my home directory
# Next, make sure 'git' is installed.
{code}
sudo yum install git
{code}
# In my home directory, I created an 'esp' subdirectory and cd'd into it.
# I then checked out the ESP code from the Git rep using:
{code}
git clone https://github.com/MBARI-ESP/ESP2Gscript.git
{code}
which creates a "ESP2Gscript" directory
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/esp/ESP2Gscript
export ESPname=neo
export ESPmode=simfast
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# by copying the *.rb files (about 4) from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/_version_
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">27066425</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">27099196</id>
<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# Clean minimal install of CentOS 7
# Git client

h3. Steps to build and run

{noformat}
# I first installed wget so I could pull down an older version of GCC.  I did this using yum:
{code}
sudo yum install wget
{code}
# Then I installed bzip2 (which is needed later) using:
{code}
sudo yum install bzip2
{code}
{noformat}
# I had to install the development tools group as well using:
{code}
sudo yum groupinstall "Development Tools"
{code}
# This installs the latest gcc, but we need version 4.6.3 installed, so I downloaded the source tar using:
{code}
wget http://ftp.gnu.org/gnu/gcc/gcc-4.6.3/gcc-4.6.3.tar.gz
{code}
# I then unzipped the download using:
{code}
gunzip gcc-4.6.3.tar.gz
{code}
# I un-tarred the file using:
{code}
tar -xvf gnu-4.6.3.tar
{code}
which created a gcc-4.6.3 directory
# I cd'd into that directory and ran
{code}
./contrib/download_prerequisites
{code}
# Once that finished, I built the gcc compiler using:
{code}
./configure --prefix=/usr/local/gcc/4.6.3
{code}
# Then run:
{code}
make
{code}
# And finally, install using:
{code}
sudo make install
{code}
# Next, you need to install the MBARI custom ruby environment.  This can be checked out of Brent Roman's Github repo by using:
{code}
git clone https://github.com/brentr/matzruby.git
{code}
which created a matzruby directory in my home directory
# Next, make sure 'git' is installed.
{code}
sudo yum install git
{code}
# In my home directory, I created an 'esp' subdirectory and cd'd into it.
# I then checked out the ESP code from the Git rep using:
{code}
git clone https://github.com/MBARI-ESP/ESP2Gscript.git
{code}
which creates a "ESP2Gscript" directory
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/esp/ESP2Gscript
export ESPname=neo
export ESPmode=simfast
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# by copying the *.rb files (about 4) from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/_version_
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">27066428</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">27099198</id>
<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# Clean minimal install of CentOS 7
# Git client

h3. Steps to build and run

{noformat}
# I first installed wget so I could pull down an older version of GCC.  I did this using yum:
{code}
sudo yum install wget
{code}
# Then I installed bzip2 (which is needed later) using:
{code}
sudo yum install bzip2
{code}
{noformat}
# I had to install the development tools group as well using:
{code}
sudo yum groupinstall "Development Tools"
{code}
{noformat}
# This installs the latest gcc, but we need version 4.6.3 installed, so I downloaded the source tar using:
{code}
wget http://ftp.gnu.org/gnu/gcc/gcc-4.6.3/gcc-4.6.3.tar.gz
{code}
# I then unzipped the download using:
{code}
gunzip gcc-4.6.3.tar.gz
{code}
# I un-tarred the file using:
{code}
tar -xvf gnu-4.6.3.tar
{code}
which created a gcc-4.6.3 directory
# I cd'd into that directory and ran
{code}
./contrib/download_prerequisites
{code}
# Once that finished, I built the gcc compiler using:
{code}
./configure --prefix=/usr/local/gcc/4.6.3
{code}
# Then run:
{code}
make
{code}
# And finally, install using:
{code}
sudo make install
{code}
{noformat}
# Next, make sure 'git' is installed.
{code}
sudo yum install git
{code}
# Next, you need to install the MBARI custom ruby environment.  This can be checked out of Brent Roman's Github repo by using:
{code}
git clone https://github.com/brentr/matzruby.git
{code}
which created a matzruby directory in my home directory
# I then cd'd into the matzruby directory and ran
{code}
git checkout esp
{code}
# Then I changed the espconfig and configure files to executable using
{code}
chmod a+x espconfig
chomd a+x configure
{code}
# In my home directory, I created an 'esp' subdirectory and cd'd into it.
# I then checked out the ESP code from the Git rep using:
{code}
git clone https://github.com/MBARI-ESP/ESP2Gscript.git
{code}
which creates a "ESP2Gscript" directory
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/esp/ESP2Gscript
export ESPname=neo
export ESPmode=simfast
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# by copying the *.rb files (about 4) from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/_version_
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">27066430</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">27099200</id>
<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# Clean minimal install of CentOS 7
# Git client

h3. Steps to build and run

{noformat}
# I first installed wget so I could pull down an older version of GCC.  I did this using yum:
{code}
sudo yum install wget
{code}
# Then I installed bzip2 (which is needed later) using:
{code}
sudo yum install bzip2
{code}
{noformat}
# I had to install the development tools group as well using:
{code}
sudo yum groupinstall "Development Tools"
{code}
# I had to install the libc devel package too
{code}
sudo yum install glibc-devel.i686
{code}
{noformat}
# This installs the latest gcc, but we need version 4.6.3 installed, so I downloaded the source tar using:
{code}
wget http://ftp.gnu.org/gnu/gcc/gcc-4.6.3/gcc-4.6.3.tar.gz
{code}
# I then unzipped the download using:
{code}
gunzip gcc-4.6.3.tar.gz
{code}
# I un-tarred the file using:
{code}
tar -xvf gnu-4.6.3.tar
{code}
which created a gcc-4.6.3 directory
# I cd'd into that directory and ran
{code}
./contrib/download_prerequisites
{code}
# Once that finished, I built the gcc compiler using:
{code}
./configure --prefix=/usr/local/gcc/4.6.3
{code}
# Then run:
{code}
make
{code}
# And finally, install using:
{code}
sudo make install
{code}
{noformat}
# Next, make sure 'git' is installed.
{code}
sudo yum install git
{code}
# Next, you need to install the MBARI custom ruby environment.  This can be checked out of Brent Roman's Github repo by using:
{code}
git clone https://github.com/brentr/matzruby.git
{code}
which created a matzruby directory in my home directory
# I then cd'd into the matzruby directory and ran
{code}
git checkout esp
{code}
# Then I changed the espconfig and configure files to executable using
{code}
chmod a+x espconfig
chomd a+x configure
{code}
# In my home directory, I created an 'esp' subdirectory and cd'd into it.
# I then checked out the ESP code from the Git rep using:
{code}
git clone https://github.com/MBARI-ESP/ESP2Gscript.git
{code}
which creates a "ESP2Gscript" directory
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/esp/ESP2Gscript
export ESPname=neo
export ESPmode=simfast
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# by copying the *.rb files (about 4) from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/_version_
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">27099202</id>
<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# Clean minimal install of CentOS 7
# Git client

h3. Steps to build and run

# I first installed wget so I could pull down an older version of GCC.  I did this using yum:
{code}
sudo yum install wget
{code}
# Then I installed bzip2 (which is needed later) using:
{code}
sudo yum install bzip2
{code}
# I had to install the development tools group as well using:
{code}
sudo yum groupinstall "Development Tools"
{code}
# I had to install the libc devel package too
{code}
sudo yum install glibc-devel.i686
{code}
# This installs the latest gcc, but we need version 4.6.3 installed, so I downloaded the source tar using:
{code}
wget http://ftp.gnu.org/gnu/gcc/gcc-4.6.3/gcc-4.6.3.tar.gz
{code}
# I then unzipped the download using:
{code}
gunzip gcc-4.6.3.tar.gz
{code}
# I un-tarred the file using:
{code}
tar -xvf gnu-4.6.3.tar
{code}
which created a gcc-4.6.3 directory
# I cd'd into that directory and ran
{code}
./contrib/download_prerequisites
{code}
# Once that finished, I built the gcc compiler using:
{code}
./configure --prefix=/usr/local/gcc/4.6.3
{code}
# Then run:
{code}
make
{code}
# And finally, install using:
{code}
sudo make install
{code}
# Next, make sure 'git' is installed.
{code}
sudo yum install git
{code}
# Next, you need to install the MBARI custom ruby environment.  This can be checked out of Brent Roman's Github repo by using:
{code}
git clone https://github.com/brentr/matzruby.git
{code}
which created a matzruby directory in my home directory
# I then cd'd into the matzruby directory and ran
{code}
git checkout esp
{code}
# Then I changed the espconfig and configure files to executable using
{code}
chmod a+x espconfig
chomd a+x configure
{code}
# In my home directory, I created an 'esp' subdirectory and cd'd into it.
# I then checked out the ESP code from the Git rep using:
{code}
git clone https://github.com/MBARI-ESP/ESP2Gscript.git
{code}
which creates a "ESP2Gscript" directory
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/esp/ESP2Gscript
export ESPname=neo
export ESPmode=simfast
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# by copying the *.rb files (about 4) from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/_version_
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">27099177</id>
<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# CVS client

h3. Steps to build and run

# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:
{code}
cvs checkout ESP/gen2/software
{code}
# &nbsp; (or if you want a branch like GUI2 (with head for anything not on branch \-f )
{code}
cvs checkout -f -r GUI2 ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# You must apply some patches by copying the *.rb files (about 4) from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/_version_
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# Clean minimal install of CentOS 7
# Git client

h3. Steps to build and run

# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:
{code}
cvs checkout ESP/gen2/software
{code}
# &nbsp; (or if you want a branch like GUI2 (with head for anything not on branch \-f )
{code}
cvs checkout -f -r GUI2 ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# You must apply some patches by copying the *.rb files (about 4) from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/_version_
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# Clean minimal install of CentOS 7
# Git client

h3. Steps to build and run

# First, make sure ruby is installed using
{code}
sudo yum install ruby
{code}
For this example, ruby 2.0.0 was installed.
# Next, make sure 'git' is installed.
{code}
sudo yum install git
{code}
# The first thing to do is get the software from the CVS repository.  You will need to have a cvs client installed and most UNIX (OS X included) comes with a command line cvs client.  We will describe that usage here.  For more information on CVS at MBARI go [here|CLT:CVS at MBARI|Click here to see more information about CVS usage at MBARI].  At the command line (after changing to the directory where you want the files to go), type:
{code}
cvs checkout ESP/gen2/software
{code}
# &nbsp; (or if you want a branch like GUI2 (with head for anything not on branch \-f )
{code}
cvs checkout -f -r GUI2 ESP/gen2/software
{code}
# You will now have the ESP/gen2/software directory where you ran the command from.  
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# You must apply some patches by copying the *.rb files (about 4) from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/_version_
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# Clean minimal install of CentOS 7
# Git client

h3. Steps to build and run

# First, make sure ruby is installed using
{code}
sudo yum install ruby
{code}
For this example, ruby 2.0.0 was installed.
# Next, make sure 'git' is installed.
{code}
sudo yum install git
{code}
# In my home directory, I created an 'esp' subdirectory and cd'd into it.
# I then checked out the ESP code from the Git rep using:
{code}
git clone https://github.com/MBARI-ESP/ESP2Gscript.git
{code}
which creates a "ESP2Gscript" directory
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/Documents/Projects/ESP/ESP/gen2/software/esp
export ESPname=neo
export ESPmode=quick
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# You must apply some patches by copying the *.rb files (about 4) from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/_version_
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr]]></property>
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<property name="body"><![CDATA[These instructions are for users who want to get the ESP control software (simulator too) up and running on their local machine.  These were written for both Red Hat (Fedora) and for Mac (Leopard) and where there are distinctions they are noted.

h3. Prerequisites

# Clean minimal install of CentOS 7
# Git client

h3. Steps to build and run

# First, make sure ruby is installed using
{code}
sudo yum install ruby
{code}
For this example, ruby 2.0.0 was installed.
# Next, make sure 'git' is installed.
{code}
sudo yum install git
{code}
# In my home directory, I created an 'esp' subdirectory and cd'd into it.
# I then checked out the ESP code from the Git rep using:
{code}
git clone https://github.com/MBARI-ESP/ESP2Gscript.git
{code}
which creates a "ESP2Gscript" directory
# To setup the ESP environment so it can run on your machine, edit your .bashrc file and add the following:
{code}
export ESPhome=/home/kgomes/esp/ESP2Gscript
export ESPname=neo
export ESPmode=simfast
export ESPpath=.:$ESPhome/mission:$ESPhome/protocol
export ESPconfigPath=$ESPhome/shallow:$ESPhome/shallow/$ESPname
export PATH=$PATH:$ESPhome/bin
export RUBYLIB="${RUBYLIB:+$RUBYLIB:}$ESPhome/lib:$ESPhome/utils:$ESPhome/protocol"
{code}
# You should then source the .bashrc (or other) file to setup the environment
# You must apply some patches by copying the *.rb files (about 4) from gen2/software/esp/ruby to /usr/lib/ruby/site_ruby/_version_
# Then you cd'd to a directory where there are mission scripts(i.e. gen2/mission) and run
{code}
esp mission.rb
{code}
where mission.rb is the mission script to be run.  This will execute the mission script and place the log file in /var/log/username.  You might have to create the /var/log/username directory and give proper permissions.
]]></property>
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<property name="body"><![CDATA[Present: Wayne, Cheri, Kevin, Jim, Doug, Scott, Chris S



h3. Machine Builds

* CBV/AIV line length is incorrect and must be changed on Betty and Gordon.&nbsp; Was changed on Moe, but core function never checked afterward.&nbsp; This issue still needs to be checked on NEO.
* Currently:
** Gordon--has MFB attached but MFB running as a stand-alone.&nbsp; Easy to merge when ready but currently Monika using MFB and core can be run seperately.
** Betty--needs thermal calibration.&nbsp; Much discussion about appropriate cold test to do, and idea is to go to \-5C, after blowing all fluid out of Burkerts with dry N2.&nbsp; Idea is to test hand, carosel, clamps, elevator, but NOT run vlaves or syringes.
** Eventually Betty needs extended chemistry tests at 2C.&nbsp; To do this we need to build larger box (rectangle) to accomodate MFB on the core.&nbsp; This box must have access door.
** MOE--needs rectangle box, because Julie is ready for cold testing of PCR.&nbsp; Moe also needs temp calibration.

h3. MFB

* John Dzenitis (LLNL) is on vacation until 6-30.&nbsp; After that they will deliver 5 modules (7-6).&nbsp; Must confirm with them our total order of 12 modules with 8 spare heater elements.

h3. Drifter

* &nbsp;

h3. Software

* Wayne taking a class at UC-B and has small class project.&nbsp; He is developing a Dwarf replacement; worried about power consumption, but looks like it may be only 20-30% higher than current dwarf, but with much more memory space.&nbsp; Wayne will talk to Scott and Brent about specifics, but class project is a go.

h3. Deep ESP/DWSM

* Benthos modem issue.&nbsp; Boards ordered to replicate Hans Thomas' junction box will not work with the newer Benthos Universal Deck box.&nbsp; Jim working with Hans and Benthos to see if there is an electronic solution to problem.
* GG is going into ball to allow DWSM testing.

h3. GUI

* Wi

h3. Deployment Issues

For J

h3. &nbsp;Other Items]]></property>
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## ESP Configuration In Lab
### Mission plan is created
### Pucks are loaded
### Reagents are loaded
### Mission script is loaded
## ESP Deployment
### Shore station is configured
#### Nothing from a GUI perspective
### FTP file store is configured
#### Once the FTP server is up and running, the user will log in to the ESP web site
#### If no mission has been created, the user creates a new mission for the ESP (can be empty)
#### The user configures the mission FTP server in the web application
##### Protocol (FTP/SFTP)
##### Server hostname
##### Port number
##### Base directory for deployment files
##### Username (or anonymous)
##### Password (or email)
##### Name and location of the log file (default is deduced from the type of mission e.g. real -> real.log)
#### The user saves the FTP configuration in web application
#### The user logs out
#### Server spins up a monitoring worker process that points to the FTP server configured for the mission
#### Process crawls FTP server site and examines each directory and file
#### If the directory/file is different that what is in the deployment directory in the ESP repository, sync file from FTP server to repository.
#### Update catalog entry for directory/file
#### If the log file was updated, spin up process to parse the log file.
### ESP mobilized on ship
#### Verify the ESP if functioning properly by checking files on the FTP station
##### Make sure ancillary instruments are logging
##### Check for any errors
##### Makes sure environment sensors are reporting that all systems are go (humidity, power, etc.)
### ESP deployed
#### Monitor ESP log files during deployment as was done in mobilization.
## ESP Operations
### ESP is sitting idle
### ESP processes sample
### ESP errors and halts
### Operator interacts with ESP
## ESP Data Analysis
### User enables image analysis
#### The proper GAL file is uploaded to the mission repository
#### The application sees the GAL file and does an automated analysis of the images.
## ESP Recovery
### Recover ESP with ship
### Demobilize the ESP off the ship
### Decommission the FTP server
### Decommission the shore station
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Data Repository]
# Interface Documents
## [Real-Time ESP state update protocol framework]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Glossary]
# [Assumptions]
# [Outstanding Questions]
# [ESP Java GUI]
# Original [ESP GUI Users Guide]

Meeting Notes
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
# [01/11/2012 *GUI Update and Planning Meeting*|2011_01_12]

Presenations for GUI Development

# [6/6/2007 PDR Powerpoint slides|^PDR.ppt]
# [6/6/2007 PDR Work breakdown spreadsheet|^PDR.xls]
{panel}
]]></property>
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<property name="body"><![CDATA[h2. For the developers

# [Getting the source|http://kahuna.shore.mbari.org/viewvc/esp/trunk/]
# [Opening in an IDE]
# [Image Processing]
# GUI Notes
## [Ruby integration]]]></property>
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## ESP Configuration In Lab
### Mission plan is created
### Pucks are loaded
### Reagents are loaded
### Mission script is loaded
## ESP Deployment
### Shore station is configured
#### Nothing from a GUI perspective
### FTP file store is configured
#### Once the FTP server is up and running, the user will log in to the ESP web site
#### If no mission has been created, the user creates a new mission for the ESP (can be empty)
#### The user configures the mission FTP server in the web application
##### Protocol (FTP/SFTP)
##### Server hostname
##### Port number
##### Base directory for deployment files
##### Username (or anonymous)
##### Password (or email)
##### Name and location of the log file (default is deduced from the type of mission e.g. real -> real.log)
#### The user saves the FTP configuration in web application
#### The user logs out
#### Server spins up a monitoring worker process that points to the FTP server configured for the mission
#### Process crawls FTP server site and examines each directory and file
#### If the directory/file is different that what is in the deployment directory in the ESP repository, sync file from FTP server to repository.
#### Update catalog entry for directory/file
#### If the log file was updated, spin up process to parse the log file.
### ESP mobilized on ship
#### Verify the ESP if functioning properly by checking files on the FTP station
##### Make sure ancillary instruments are logging
##### Check for any errors
##### Makes sure environment sensors are reporting that all systems are go (humidity, power, etc.)
### ESP deployed
#### Monitor ESP log files during deployment as was done in mobilization.
## ESP Operations
### ESP is sitting idle
### ESP processes sample
### ESP errors and halts
### Operator interacts with ESP
## ESP Data Analysis
### User enables image analysis
#### The proper GAL file is uploaded to the mission repository
#### The application sees the GAL file and does an automated analysis of the images.
## ESP Recovery
### Recover ESP with ship
### Demobilize the ESP off the ship
### Decommission the FTP server
### Decommission the shore station
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Data Repository]
# Interface Documents
## [Real-Time ESP state update protocol framework]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Glossary]
# [Assumptions]
# [Outstanding Questions]
# [ESP Java GUI]
# Original [ESP GUI Users Guide]

Meeting Notes
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
# [01/11/2012 *GUI Update and Planning Meeting*|2011_01_12]
{panel}
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## ESP Configuration In Lab
### Mission plan is created
### Pucks are loaded
### Reagents are loaded
### Mission script is loaded
## ESP Deployment
### Shore station is configured
#### Nothing from a GUI perspective
### FTP file store is configured
#### Once the FTP server is up and running, the user will log in to the ESP web site
#### If no mission has been created, the user creates a new mission for the ESP (can be empty)
#### The user configures the mission FTP server in the web application
##### Protocol (FTP/SFTP)
##### Server hostname
##### Port number
##### Base directory for deployment files
##### Username (or anonymous)
##### Password (or email)
##### Name and location of the log file (default is deduced from the type of mission e.g. real -> real.log)
#### The user saves the FTP configuration in web application
#### The user logs out
#### Server spins up a monitoring worker process that points to the FTP server configured for the mission
#### Process crawls FTP server site and examines each directory and file
#### If the directory/file is different that what is in the deployment directory in the ESP repository, sync file from FTP server to repository.
#### Update catalog entry for directory/file
#### If the log file was updated, spin up process to parse the log file.
### ESP mobilized on ship
#### Verify the ESP if functioning properly by checking files on the FTP station
##### Make sure ancillary instruments are logging
##### Check for any errors
##### Makes sure environment sensors are reporting that all systems are go (humidity, power, etc.)
### ESP deployed
#### Monitor ESP log files during deployment as was done in mobilization.
## ESP Operations
### ESP is sitting idle
### ESP processes sample
### ESP errors and halts
### Operator interacts with ESP
## ESP Data Analysis
### User enables image analysis
#### The proper GAL file is uploaded to the mission repository
#### The application sees the GAL file and does an automated analysis of the images.
## ESP Recovery
### Recover ESP with ship
### Demobilize the ESP off the ship
### Decommission the FTP server
### Decommission the shore station
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# Interface Documents
## [Real-Time ESP state update protocol framework]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Data Repository]
# [Developer Documentation]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Glossary]
# [Assumptions]
# [Outstanding Questions]
# [ESP Java GUI]
# Original [ESP GUI Users Guide]

Meeting Notes
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
# [01/11/2012 *GUI Update and Planning Meeting*|2011_01_12]

Presenations for GUI Development

# [6/6/2007 PDR Powerpoint slides|^PDR.ppt]
# [6/6/2007 PDR Work breakdown spreadsheet|^PDR.xls]
{panel}
]]></property>
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## ESP Configuration In Lab
### Mission plan is created
### Pucks are loaded
### Reagents are loaded
### Mission script is loaded
## ESP Deployment
### Shore station is configured
#### Nothing from a GUI perspective
### FTP file store is configured
#### Once the FTP server is up and running, the user will log in to the ESP web site
#### If no mission has been created, the user creates a new mission for the ESP (can be empty)
#### The user configures the mission FTP server in the web application
##### Protocol (FTP/SFTP)
##### Server hostname
##### Port number
##### Base directory for deployment files
##### Username (or anonymous)
##### Password (or email)
##### Name and location of the log file (default is deduced from the type of mission e.g. real -> real.log)
#### The user saves the FTP configuration in web application
#### The user logs out
#### Server spins up a monitoring worker process that points to the FTP server configured for the mission
#### Process crawls FTP server site and examines each directory and file
#### If the directory/file is different that what is in the deployment directory in the ESP repository, sync file from FTP server to repository.
#### Update catalog entry for directory/file
#### If the log file was updated, spin up process to parse the log file.
### ESP mobilized on ship
#### Verify the ESP if functioning properly by checking files on the FTP station
##### Make sure ancillary instruments are logging
##### Check for any errors
##### Makes sure environment sensors are reporting that all systems are go (humidity, power, etc.)
### ESP deployed
#### Monitor ESP log files during deployment as was done in mobilization.
## ESP Operations
### ESP is sitting idle
### ESP processes sample
### ESP errors and halts
### Operator interacts with ESP
## ESP Data Analysis
### User enables image analysis
#### The proper GAL file is uploaded to the mission repository
#### The application sees the GAL file and does an automated analysis of the images.
## ESP Recovery
### Recover ESP with ship
### Demobilize the ESP off the ship
### Decommission the FTP server
### Decommission the shore station
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Glossary]
# [Assumptions]
# [Outstanding Questions]
# [ESP Java GUI]
# Original [ESP GUI Users Guide]

Meeting Notes
## [06/06/2007 *PDR*|Project Memos Minutes]
## [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
## [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
## [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
## [01/08/2008 *Resources and Consumables*|2008_01_08]
## [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
## [01/22/2009 *GUI Team Meeting*|2009_01_22]
## [01/11/2012 *GUI Update and Planning Meeting*|2011_01_12]
{panel}
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<id name="id">27099277</id>
<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## ESP Configuration In Lab
### Mission plan is created
### Pucks are loaded
### Reagents are loaded
### Mission script is loaded
## ESP Deployment
### Shore station is configured
#### Nothing from a GUI perspective
### FTP file store is configured
#### Once the FTP server is up and running, the user will log in to the ESP web site
#### If no mission has been created, the user creates a new mission for the ESP (can be empty)
#### The user configures the mission FTP server in the web application
##### Protocol (FTP/SFTP)
##### Server hostname
##### Port number
##### Base directory for deployment files
##### Username (or anonymous)
##### Password (or email)
##### Name and location of the log file (default is deduced from the type of mission e.g. real -> real.log)
#### The user saves the FTP configuration in web application
#### The user logs out
#### Server spins up a monitoring worker process that points to the FTP server configured for the mission
#### Process crawls FTP server site and examines each directory and file
#### If the directory/file is different that what is in the deployment directory in the ESP repository, sync file from FTP server to repository.
#### Update catalog entry for directory/file
#### If the log file was updated, spin up process to parse the log file.
### ESP mobilized on ship
#### Verify the ESP if functioning properly by checking files on the FTP station
##### Make sure ancillary instruments are logging
##### Check for any errors
##### Makes sure environment sensors are reporting that all systems are go (humidity, power, etc.)
### ESP deployed
#### Monitor ESP log files during deployment as was done in mobilization.
## ESP Operations
### ESP is sitting idle
### ESP processes sample
### ESP errors and halts
### Operator interacts with ESP
## ESP Data Analysis
### User enables image analysis
#### The proper GAL file is uploaded to the mission repository
#### The application sees the GAL file and does an automated analysis of the images.
## ESP Recovery
### Recover ESP with ship
### Demobilize the ESP off the ship
### Decommission the FTP server
### Decommission the shore station
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Glossary]
# [Assumptions]
# [Outstanding Questions]
# [ESP Java GUI]
# Original [ESP GUI Users Guide]

# Meeting Notes
## [06/06/2007 *PDR*|Project Memos Minutes]
## [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
## [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
## [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
## [01/08/2008 *Resources and Consumables*|2008_01_08]
## [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
## [01/22/2009 *GUI Team Meeting*|2009_01_22]
## [01/11/2012 *GUI Update and Planning Meeting*|2011_01_12]
{panel}
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## ESP Configuration In Lab
### Mission plan is created
### Pucks are loaded
### Reagents are loaded
### Mission script is loaded
## ESP Deployment
### Shore station is configured
#### Nothing from a GUI perspective
### FTP file store is configured
#### Once the FTP server is up and running, the user will log in to the ESP web site
#### If no mission has been created, the user creates a new mission for the ESP (can be empty)
#### The user configures the mission FTP server in the web application
##### Protocol (FTP/SFTP)
##### Server hostname
##### Port number
##### Base directory for deployment files
##### Username (or anonymous)
##### Password (or email)
##### Name and location of the log file (default is deduced from the type of mission e.g. real -> real.log)
#### The user saves the FTP configuration in web application
#### The user logs out
#### Server spins up a monitoring worker process that points to the FTP server configured for the mission
#### Process crawls FTP server site and examines each directory and file
#### If the directory/file is different that what is in the deployment directory in the ESP repository, sync file from FTP server to repository.
#### Update catalog entry for directory/file
#### If the log file was updated, spin up process to parse the log file.
### ESP mobilized on ship
#### Verify the ESP if functioning properly by checking files on the FTP station
##### Make sure ancillary instruments are logging
##### Check for any errors
##### Makes sure environment sensors are reporting that all systems are go (humidity, power, etc.)
### ESP deployed
#### Monitor ESP log files during deployment as was done in mobilization.
## ESP Operations
### ESP is sitting idle
### ESP processes sample
### ESP errors and halts
### Operator interacts with ESP
## ESP Data Analysis
### User enables image analysis
#### The proper GAL file is uploaded to the mission repository
#### The application sees the GAL file and does an automated analysis of the images.
## ESP Recovery
### Recover ESP with ship
### Demobilize the ESP off the ship
### Decommission the FTP server
### Decommission the shore station
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Glossary]
# [Assumptions]
# [Outstanding Questions]
# [ESP Java GUI]
# Original [ESP GUI Users Guide]
{panel}
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## ESP Configuration In Lab
### Mission plan is created
### Pucks are loaded
### Reagents are loaded
### Mission script is loaded
## ESP Deployment
### Shore station is configured
#### Nothing from a GUI perspective
### FTP file store is configured
#### Once the FTP server is up and running, the user will log in to the ESP web site
#### If no mission has been created, the user creates a new mission for the ESP (can be empty)
#### The user configures the mission FTP server in the web application
##### Protocol (FTP/SFTP)
##### Server hostname
##### Port number
##### Base directory for deployment files
##### Username (or anonymous)
##### Password (or email)
##### Name and location of the log file (default is deduced from the type of mission e.g. real -> real.log)
#### The user saves the FTP configuration in web application
#### The user logs out
#### Server spins up a monitoring worker process that points to the FTP server configured for the mission
#### Process crawls FTP server site and examines each directory and file
#### If the directory/file is different that what is in the deployment directory in the ESP repository, sync file from FTP server to repository.
#### Update catalog entry for directory/file
#### If the log file was updated, spin up process to parse the log file.
### ESP mobilized on ship
#### Verify the ESP if functioning properly by checking files on the FTP station
##### Make sure ancillary instruments are logging
##### Check for any errors
##### Makes sure environment sensors are reporting that all systems are go (humidity, power, etc.)
### ESP deployed
#### Monitor ESP log files during deployment as was done in mobilization.
## ESP Operations
### ESP is sitting idle
### ESP processes sample
### ESP errors and halts
### Operator interacts with ESP
## ESP Data Analysis
### User enables image analysis
#### The proper GAL file is uploaded to the mission repository
#### The application sees the GAL file and does an automated analysis of the images.
## ESP Recovery
### Recover ESP with ship
### Demobilize the ESP off the ship
### Decommission the FTP server
### Decommission the shore station
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [ESP Java GUI]
# Original [ESP GUI Users Guide]
{panel}
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## ESP Configuration In Lab
### Mission plan is created
### Pucks are loaded
### Reagents are loaded
### Mission script is loaded
## ESP Deployment
### Shore station is configured
#### Nothing from a GUI perspective
### FTP file store is configured
#### Once the FTP server is up and running, the user will log in to the ESP web site
#### If no mission has been created, the user creates a new mission for the ESP (can be empty)
#### The user configures the mission FTP server in the web application
##### Protocol (FTP/SFTP)
##### Server hostname
##### Port number
##### Base directory for deployment files
##### Username (or anonymous)
##### Password (or email)
##### Name and location of the log file (default is deduced from the type of mission e.g. real -> real.log)
#### The user saves the FTP configuration in web application
#### The user logs out
#### Server spins up a monitoring worker process that points to the FTP server configured for the mission
#### Process crawls FTP server site and examines each directory and file
#### If the directory/file is different that what is in the deployment directory in the ESP repository, sync file from FTP server to repository.
#### Update catalog entry for directory/file
#### If the log file was updated, spin up process to parse the log file.
### ESP mobilized on ship
#### Verify the ESP if functioning properly by checking files on the FTP station
##### Make sure ancillary instruments are logging
##### Check for any errors
##### Makes sure environment sensors are reporting that all systems are go (humidity, power, etc.)
### ESP deployed
#### Monitor ESP log files during deployment as was done in mobilization.
## ESP Operations
### ESP is sitting idle
### ESP processes sample
### ESP errors and halts
### Operator interacts with ESP
## ESP Data Analysis
### User enables image analysis
#### The proper GAL file is uploaded to the mission repository
#### The application sees the GAL file and does an automated analysis of the images.
## ESP Recovery
### Recover ESP with ship
### Demobilize the ESP off the ship
### Decommission the FTP server
### Decommission the shore station
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Data Repository]
# Interface Documents
## [Real-Time ESP state update protocol framework]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Glossary]
# [Assumptions]
# [Outstanding Questions]
# [ESP Java GUI]
# Original [ESP GUI Users Guide]

Meeting Notes
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
# [01/11/2012 *GUI Update and Planning Meeting*|2011_01_12]
{panel}
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## ESP Configuration In Lab
### Mission plan is created
### Pucks are loaded
### Reagents are loaded
### Mission script is loaded
## ESP Deployment
### Shore station is configured
#### Nothing from a GUI perspective
### FTP file store is configured
#### Once the FTP server is up and running, the user will log in to the ESP web site
#### If no mission has been created, the user creates a new mission for the ESP (can be empty)
#### The user configures the mission FTP server in the web application
##### Protocol (FTP/SFTP)
##### Server hostname
##### Port number
##### Base directory for deployment files
##### Username (or anonymous)
##### Password (or email)
##### Name and location of the log file (default is deduced from the type of mission e.g. real -> real.log)
#### The user saves the FTP configuration in web application
#### The user logs out
#### Server spins up a monitoring worker process that points to the FTP server configured for the mission
#### Process crawls FTP server site and examines each directory and file
#### If the directory/file is different that what is in the deployment directory in the ESP repository, sync file from FTP server to repository.
#### Update catalog entry for directory/file
#### If the log file was updated, spin up process to parse the log file.
### ESP mobilized on ship
#### Verify the ESP if functioning properly by checking files on the FTP station
##### Make sure ancillary instruments are logging
##### Check for any errors
##### Makes sure environment sensors are reporting that all systems are go (humidity, power, etc.)
### ESP deployed
#### Monitor ESP log files during deployment as was done in mobilization.
## ESP Operations
### ESP is sitting idle
### ESP processes sample
### ESP errors and halts
### Operator interacts with ESP
## ESP Data Analysis
### User enables image analysis
#### The proper GAL file is uploaded to the mission repository
#### The application sees the GAL file and does an automated analysis of the images.
## ESP Recovery
### Recover ESP with ship
### Demobilize the ESP off the ship
### Decommission the FTP server
### Decommission the shore station
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Glossary]
# [Assumptions]
# [Outstanding Questions]
# [ESP Java GUI]
# Original [ESP GUI Users Guide]

Meeting Notes
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
# [01/11/2012 *GUI Update and Planning Meeting*|2011_01_12]
{panel}
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<property name="body"><![CDATA[In order to gather the requirements for the Graphical User Interface, the GUI team met with the ESP science and engineering members to try to determine what the GUI needs to do.  We also poured over relevant documentation to try to extract as much knowledge as we could about the system before defining the requirements (see below).  The following requirements were gathered as part of that process.

h3. Requirements
|| Number || Requirement || Goal ||
| | User can define missions by specifying phases | Planning |
| | User can specify and adjust phase start times | Planning |
| | User can also specify a time to wait between events instead of a specific start time | Planning |
| | User can set mission start and end times that are not associated with a phase/protocol | Planning |
| | User can specify comments associated with missions that are printed at the top of the mission script | Planning |
| | After planning, application should generate mission script, puck loads, and reagent volumes | Planning |
| | User can add comments to a phase that will be generated in the script | Planning |
| | Users can add/delete/edit protocol runs and phases | Planning |
| | Users can load missions from existing ruby scripts | Planning |
| | Users can specify thresholding events in plans ([example|Mission Planning Script with Thresholding]) | Planning |
| | Users can copy existing phase and protocol to crate duplicate | Planning |
| | Users can add/delete/edit consumables | Planning |
| | Users can schedule Kills (end purges) or disable kills | Planning |
| | Users can define generic events and what script will actually be added to the master script (if needed) | Planning |
| | Mission plan generation will include a puck loading list | Planning |
| | User can associate external files with events (excel spreadsheet, documents, etc.) | Planning, Data Management |
| | Tide and phase information will be available | Planning, Data Management |
| | Application will list sample volumes with protocol run | Planning, Data Management |
| | User can add non-phase/protocol events (user defined) to the calendar anywhere | Data Management |
| | User can view images associated with phases | Data Management |
| | User can browse the .GAL file along with image and filter paper information | Data Management |
| | User can browse image, click on intensity and application applies .GAL/Map with standard curves to give density | Data Management |
| | User can browse the low-res images that come over the telemetry until full size image is offloaded after recovery | Data Management |
| | When users selects a protocol run/phase, the contextual data (CTD/ISUS) should be shown | Data Management |
| | Application should allow for details of flushes to be seen/accounted for | Data Management |
| | The application should archive (and make available) the environment variables for each deployment and make available to user.  These variables are:
# _ESPhome_: Is the directory on the linux host which is the top level (root) of the directory of ESP source code tree
# _ESPname_: is the name of the ESP machine
# _ESPmode_: is the operating mode in which to run the ESP software
# _ESPlog_: is the root directory on the linux host under which all data files are written.
# _ESPpath_: is a list of directories on the linux host to search for mission scripts.
# _ESPconfigPath_: is a list of directories to search for configuration files.  The path will include the ESPtype which is either shallow, mfb, 1km, or 4km.
# _RUBYLIB_: is a list of directories to search for the "required" Ruby libraries and scripts | Data Management |
| | Users should be able to download instrument logs and images and the GUI will parse out the following events:
* Track deployments of contextual sensors (sub-deployments of ESP)
* Collection of contextual sensor data (with capability to view/work with data) 
* Phase Start Time
* Start Time of Initial Purge (what version if there is one)
* End Time of Initial Purge (what version if there is one)
* Start Time of SH1 (Protocol for sample collection/homogenization)
* Start Time of Actual Sample Collection for SH1
* End Time of Sample Collection for SH1
* Volume of Sample Collected
* End Time of SH1
* Start Time of SH2 Protocol (Generally preceeds end of SH1)
* Start Time of WCR (Generally preceeds end of SH2)
* Start Time of Actual Sample for WCR
* End Time of Sample Collection for WCR
* Array Images (Generally >1 and >1 resolution/binning, exposure times)
* End of SH2
* End of WCR
* Start Time of final purge (what version, if there is one)
* End Time of final purge (what version, if there is one)
* Phase End Time | Data Management, State Visualization |
| | Application will track status of consumables:
# Pucks
# Reagents: 20 or so
# Waste
# Power | State Visualization |
| | Users can visualize the current state of the instrument | State Visualization |
| | Users can scroll back in time and visualize instrument state at the various points in time | State Visualization |

h5. Information Sources
{section}
{column:width=50%}
{panel:title=Supporting Docs}
# [Slides From a Tour Geared towards Engineers|^engineeringTour.pdf]
# [Slides from a User Manual meeting that was an overview of the ESP|^overview.pdf]
# [Slides from a User Manual meeting about the Operating Environment of the ESP|^ESPenviroment.pdf]
# [Slides from a User Manual meeting about the users and groups in the ESP operating system|^usersAndGroups.pdf]
# [Slides from a User Manual meeting about the Core Libraries for the ESP|^ESPcoreLib.pdf]
# [Slides from a User Manual meeting about I2C and its use in the ESP|^ESPi2c.pdf]
# [Slides from a User Manual meeting about the servos in the ESP|^ESPservos.pdf]
# [Slides from a User Manual meeting about the slides in the ESP|^ESPslide.pdf]
# [Slides from a User Manual meeting about the Axes in the ESP|^ESPaxes.pdf]
# [Slides from a User Manual meeting about the parameters used in operating the ESP|^ESPparams.pdf]
# [Slides from a User Manual meeting about contextual sensors|^ESPsensors.pdf]
# [Slides from a User Manual meeting about the shore side components of the ESP|^ESPshore.pdf]
# [Slides from a User Manual meeting about errors and error handling|^ESPerrors.pdf]
# [ESP Fluidics Schematic|^ESP Fluidics v2_2 small.pdf]
# [ESP Users Manual|^ESPManual_v1.pdf]
# [Glossary]
# [Assumptions]
# [Outstanding Questions]
{panel}
{column}
{column:width=50%}
{panel:title=Meeting Notes}
# [06/06/2007 *PDR*|Project Memos Minutes]
# [06/11/2007 *Meet with Chris*|Meeting with Chris, June 11, 2007]
# [09/05/2007 *ESP GUI Demo and Questions*|2007_09_05]
# [09/07/2007 *Scholin email*|^ESPGUIDMthingstotrackextractfromlog.htm]
# [01/08/2008 *Resources and Consumables*|2008_01_08]
# [03/11/2008 *Mock Mission Planning Meeting*|2008_03_11]
# [01/22/2009 *GUI Team Meeting*|2009_01_22]
# [01/11/2012 *GUI Update and Planning Meeting*|2011_01_12]
{panel}
{column}
{section}
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## ESP Configuration In Lab
### Mission plan is created
### Pucks are loaded
### Reagents are loaded
### Mission script is loaded
## ESP Deployment
### Shore station is configured
#### Nothing from a GUI perspective
### FTP file store is configured
#### Once the FTP server is up and running, the user will log in to the ESP web site
#### If no mission has been created, the user creates a new mission for the ESP (can be empty)
#### The user configures the mission FTP server in the web application
##### Protocol (FTP/SFTP)
##### Server hostname
##### Port number
##### Base directory for deployment files
##### Username (or anonymous)
##### Password (or email)
##### Name and location of the log file (default is deduced from the type of mission e.g. real -> real.log)
#### The user saves the FTP configuration in web application
#### The user logs out
#### Server spins up a monitoring worker process that points to the FTP server configured for the mission
#### Process crawls FTP server site and examines each directory and file
#### If the directory/file is different that what is in the deployment directory in the ESP repository, sync file from FTP server to repository.
#### Update catalog entry for directory/file
#### If the log file was updated, spin up process to parse the log file.
### ESP mobilized on ship
#### Verify the ESP if functioning properly by checking files on the FTP station
##### Make sure ancillary instruments are logging
##### Check for any errors
##### Makes sure environment sensors are reporting that all systems are go (humidity, power, etc.)
### ESP deployed
#### Monitor ESP log files during deployment as was done in mobilization.
## [ESP Operations]
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [ESP Java GUI]
# Original [ESP GUI Users Guide]
{panel}
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## ESP Configuration In Lab
### Mission plan is created
### Pucks are loaded
### Reagents are loaded
### Mission script is loaded
## [ESP Deployment]
## [ESP Operations]
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [ESP Java GUI]
# Original [ESP GUI Users Guide]
{panel}
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<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## ESP Configuration In Lab
### Mission plan is created
### Pucks are loaded
### Reagents are loaded
### Mission script is loaded
## ESP Deployment
### Shore station is configured
#### Nothing from a GUI perspective
### FTP file store is configured
#### Once the FTP server is up and running, the user will log in to the ESP web site
#### If no mission has been created, the user creates a new mission for the ESP (can be empty)
#### The user configures the mission FTP server in the web application
##### Protocol (FTP/SFTP)
##### Server hostname
##### Port number
##### Base directory for deployment files
##### Username (or anonymous)
##### Password (or email)
##### Name and location of the log file (default is deduced from the type of mission e.g. real -> real.log)
#### The user saves the FTP configuration in web application
#### The user logs out
#### Server spins up a monitoring worker process that points to the FTP server configured for the mission
#### Process crawls FTP server site and examines each directory and file
#### If the directory/file is different that what is in the deployment directory in the ESP repository, sync file from FTP server to repository.
#### Update catalog entry for directory/file
#### If the log file was updated, spin up process to parse the log file.
### ESP mobilized on ship
#### Verify the ESP if functioning properly by checking files on the FTP station
##### Make sure ancillary instruments are logging
##### Check for any errors
##### Makes sure environment sensors are reporting that all systems are go (humidity, power, etc.)
### ESP deployed
#### Monitor ESP log files during deployment as was done in mobilization.
## ESP Operations
### ESP is sitting idle
### ESP processes sample
### ESP errors and halts
### Operator interacts with ESP
## ESP Data Analysis
### User enables image analysis
#### The proper GAL file is uploaded to the mission repository
#### The application sees the GAL file and does an automated analysis of the images.
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [ESP Java GUI]
# Original [ESP GUI Users Guide]
{panel}
]]></property>
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<id name="id">27099272</id>
<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## ESP Configuration In Lab
### Mission plan is created
### Pucks are loaded
### Reagents are loaded
### Mission script is loaded
## ESP Deployment
### Shore station is configured
#### Nothing from a GUI perspective
### FTP file store is configured
#### Once the FTP server is up and running, the user will log in to the ESP web site
#### If no mission has been created, the user creates a new mission for the ESP (can be empty)
#### The user configures the mission FTP server in the web application
##### Protocol (FTP/SFTP)
##### Server hostname
##### Port number
##### Base directory for deployment files
##### Username (or anonymous)
##### Password (or email)
##### Name and location of the log file (default is deduced from the type of mission e.g. real -> real.log)
#### The user saves the FTP configuration in web application
#### The user logs out
#### Server spins up a monitoring worker process that points to the FTP server configured for the mission
#### Process crawls FTP server site and examines each directory and file
#### If the directory/file is different that what is in the deployment directory in the ESP repository, sync file from FTP server to repository.
#### Update catalog entry for directory/file
#### If the log file was updated, spin up process to parse the log file.
### ESP mobilized on ship
#### Verify the ESP if functioning properly by checking files on the FTP station
##### Make sure ancillary instruments are logging
##### Check for any errors
##### Makes sure environment sensors are reporting that all systems are go (humidity, power, etc.)
### ESP deployed
#### Monitor ESP log files during deployment as was done in mobilization.
## ESP Operations
### ESP is sitting idle
### ESP processes sample
### ESP errors and halts
### Operator interacts with ESP
## ESP Data Analysis
### User enables image analysis
#### The proper GAL file is uploaded to the mission repository
#### The application sees the GAL file and does an automated analysis of the images.## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [ESP Java GUI]
# Original [ESP GUI Users Guide]
{panel}
]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">27099271</id>
<property name="body"><![CDATA[{panel:title=Current Applications}
# [Web application|http://services.mbari.org/espweb/#]
# [Image Analysis|https://bitbucket.org/mbari/esp-image-analysis/overview]
{panel}
{panel:title=User Documentation}
# [Image Analysis Application|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Application]
# [Image Analysis Automation|https://oceana.mbari.org/confluence/display/ESPAPP/ESP+Image+Analysis+Automation]
{panel}
{panel:title=Design Documentation}
# The goals for the ESP GUI Application are:
## A graphical interface to allow the user to plan a mission for the ESP
## The GUI can take a mission plan and generate a valid mission script to deploy on the ESP
## The GUI will provide functionality to manage the data from the ESP.  This data consists of:
### Various Ruby scripts
### Image analysis of the probe arrays
### Ancillary instrument data
### Events and data from log file (parsing)
## The GUI will provide a visual representation of the state of the ESP
### Currently user has to look through log file and mentally visualize state of system
### GUI should display visual representation of the instrument and its components
### Take instrument state from log file and produce graphical representation that will depict the current state of the instrument
### The state visualization should be able to playback a mission run from a log file and step the user through instrument states
## The GUI application should be focused on transitioning the ESP to a user community (not necessarily a development community)
# Use Cases
## ESP Configuration In Lab
### Mission plan is created
### Pucks are loaded
### Reagents are loaded
### Mission script is loaded
## ESP Deployment
### Shore station is configured
#### Nothing from a GUI perspective
### FTP file store is configured
#### Once the FTP server is up and running, the user will log in to the ESP web site
#### If no mission has been created, the user creates a new mission for the ESP (can be empty)
#### The user configures the mission FTP server in the web application
##### Protocol (FTP/SFTP)
##### Server hostname
##### Port number
##### Base directory for deployment files
##### Username (or anonymous)
##### Password (or email)
##### Name and location of the log file (default is deduced from the type of mission e.g. real -> real.log)
#### The user saves the FTP configuration in web application
#### The user logs out
#### Server spins up a monitoring worker process that points to the FTP server configured for the mission
#### Process crawls FTP server site and examines each directory and file
#### If the directory/file is different that what is in the deployment directory in the ESP repository, sync file from FTP server to repository.
#### Update catalog entry for directory/file
#### If the log file was updated, spin up process to parse the log file.
### ESP mobilized on ship
#### Verify the ESP if functioning properly by checking files on the FTP station
##### Make sure ancillary instruments are logging
##### Check for any errors
##### Makes sure environment sensors are reporting that all systems are go (humidity, power, etc.)
### ESP deployed
#### Monitor ESP log files during deployment as was done in mobilization.
## ESP Operations
### ESP is sitting idle
### ESP processes sample
### ESP errors and halts
### Operator interacts with ESP
## [ESP Data Analysis]
## [ESP Recovery]
# [Requirements|Requirements (and Gathering) Documentation]
## [Assumptions|ESPAPP:Assumptions]
## [Glossary]
## [Open Questions|ESPAPP:Outstanding Questions|Questions that are still open for GUI development]
# [GUI Application Design|Design]
## [Object Model]
## [Data Model]
## [Real-Time ESP state update protocol framework]
## [Data Repository]
# [Presentations|ProjectPresentations]
# [Developer Documentation]
## [ESP Log Interface|ESPAPP:ESP Log Interface|The interface for dealing with the ESP log files]
### [Parsing the ESP log file|ESPAPP:Parsing the Raw ESP Log File Format|Information about how to parse the ESP log files]
# [Development Log]
{panel}
{panel:title=Outstanding Issues}
[Bug Tracking|https://github.com/kgomes/esp-apps/issues]
{panel}
{panel:title=Supporting Documentation}
# [GUI Related Proposals]
# [ESP Java GUI]
# Original [ESP GUI Users Guide]
{panel}
]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387879</id>
<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically+

April 6--Bruce at M0 for surface deployment (Zephyr)

April 15--Mack in Sphere for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

April 29--Recover Bruce at M0 (Zephyr)

May 1--Mack in sphere connected to DWSM(dive #3); incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

May 14--Deploy NEO w/PCR, surface deployment (Zephyr)

May 27--First Drifter dive (Zephyr)

June 5-9 \-\- Western Flyer.&nbsp; D-ESP, Drifter, and CTD casts.  D-ESP launch is here.  Drifter launch is here.

June 11 \-\- Recover NEO.&nbsp; (Zephyr) ]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387880</id>
<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically+

April 6--Bruce at M0 for surface deployment (Zephyr)

April 15--Mack in Sphere for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

April 29--Recover Bruce at M0 (Zephyr)

May 1--Mack in sphere connected to DWSM(dive #3); incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

May 14--Deploy NEO w/PCR, surface deployment (Zephyr)

May 27--First Drifter dive (Zephyr)

June 5-9 \-\- Western Flyer.&nbsp; D-ESP, Drifter, and CTD casts.  D-ESP launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/DESP%deployment%(full%quality).dv].  Drifter launch is here.

June 11 \-\- Recover NEO.&nbsp; (Zephyr) 

[System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10355143</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387882</id>
<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically+

April 6--Bruce at M0 for surface deployment (Zephyr)

April 15--Mack in Sphere for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

April 29--Recover Bruce at M0 (Zephyr)

May 1--Mack in sphere connected to DWSM(dive #3); incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

May 14--Deploy NEO w/PCR, surface deployment (Zephyr)

May 27--First Drifter dive (Zephyr)

June 5-9 \-\- Western Flyer.&nbsp; D-ESP, Drifter, and CTD casts.  D-ESP launch is [here |http://mww.mbari.org/ProjectLibrary/ESP/Movies/DESP%20deployment%20(full%20quality).dv].  Drifter launch is here.

June 11 \-\- Recover NEO.&nbsp; (Zephyr)

[System tubing diagram (updated 04 Dec 2008) |http://mww.mbari.org/ProjectLibrary/ESP/2G/Project.Drawings/Project.ME.Dwgs/Fluidics%20worksheet%2004Dec08.pdf]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10355145</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10387877</id>
<property name="body"><![CDATA[h3. +These are deployments+ +during 2009+ +arranged chronologically+

April 6--Bruce at M0 for surface deployment (Zephyr)

April 15--Mack in Sphere for first D-ESP engineering dive < {color:#ff0000}cruise CANCELED because of wind{color}\\

April 23--Mack deployed in sphere (dive #2) off Lobos.&nbsp; Took it to ~ 700m.&nbsp; One DWSM pump was non-functional.&nbsp; Doug later discovered fuzz from bag was caught in impeller.

April 29--Recover Bruce at M0 (Zephyr)

May 1--Mack in sphere connected to DWSM(dive #3); incredible success.&nbsp; Nat Geo filmed dive. (Lobos)

May 14--Deploy NEO w/PCR, surface deployment (Zephyr)

May 27--First Drifter dive (Zephyr)

June 5-9 \-\- Western Flyer.&nbsp; D-ESP, Drifter, and CTD casts.

June 11 \-\- Recover NEO.&nbsp; (Zephyr) ]]></property>
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<property name="body"><![CDATA[# [08Jan2009]
# [15Jan2009]
# [22Jan2009]
# 29Jan2009 - no meeting; ASLO
# [05Feb2009]
# [12Feb2009]
# [19Feb2009]
# [26Feb2009]
# [05Mar2009] \--First drifter attendance
# [12Mar2009] \--crew and machine assignments for upcoming deployments
# [19Mar2009]
# [26Mar2009]
# 02Apr2009 \--Jim in DC
# [09Apr2009]
# [16Apr2009]
# 23Apr2009 - no meeting; first D-ESP deployment
# 30Apr2009 - no meeting; final D-ESP deployment tomorrow
# [07May2009]
# [14May2009]
# [21May2009] \--2-week plan leading to Flyer deployment
# [28May2009]
# 04Jun2009 - no meeting; Flyer deployment
# 11Jun2009 - no meeting; Neo recovery with Zephyr
# [16Jun2009] \--Axial cruise decision]]></property>
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<property name="name"><![CDATA[favourite]]></property>
<property name="owner"><![CDATA[everlove]]></property>
<property name="namespace"><![CDATA[my]]></property>
<property name="creationDate">2008-02-27 07:57:15.067</property>
<property name="lastModificationDate">2008-02-27 07:57:15.087</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">7209000</id>
<property name="body"><![CDATA[*Regarding Bruce's post can QC errors:*

&nbsp;Roman and I now believe that the camera seal did not go to the DA puck

rather than the other way 'round :-) &nbsp; If you look at the high-res image

&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; shortDA08oct2909h100ml70s.tif

one can plainly see that the puck is bright and blurry, but the filter spots

are in focus.&nbsp; Is it possible that the camera seal spring loaded seal mechanism

got stuck?&nbsp; Note that, if this were to happen in the can, we probably would not

even notice it, as it would be already very dark in there anyway.\\

If we don't think the mechanism got stuck, we should do some tests do determine

how far out of position the elevator would have to be to yield an image like the

one observed.&nbsp;&nbsp; (spots in focus with puck body clearly visible)
\\

*Regarding Mack's hand being unable to pull the flush puck from its garage*:

&nbsp;The forearm was barely moving with high current levels when these errors occurred.

Recall the the current limit on the Forearm axis is set so high that an overcurrent cannot

occur unless the motor short circuits.&nbsp; The upshot is that the forearm was stuck.

Could the ball bearing spring mechanism that holds the flushpuck in place be sticking

in the "up" position?&nbsp;

We've seen this before...&nbsp;\\

&nbsp;@08:49:14.96@<manipulator>I2C::Servo::AbsMoveQuery\[37:20->26\]#0 to 2650
@08:49:15.68@<core>I2C::Servo::AbsMoveReply\[37:26->20\] trajectoryErr with status:
<enabled=false, pastRLS=false, pastFLS=false, pastThreshold=false, lost=false, home=false, position=-11623, velocity=20, current=162, pwm=nil, sum=nil, inPress=147, outPress=147, voltage=nil>
@08:49:15.70@<MAIN>Slide::Error: Forearm trajectoryErr
@08:49:15.73@Retry #1 of 3
...
\\ \\]]></property>
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<property name="body"><![CDATA[4.  Investigate remaining puck handling problems warm and cold

&nbsp;&nbsp;&nbsp; a. still seeing Elbow errors even when Forearm not pressing puck against backstop

5.  Add software check to ensure mission continuations start tube matches last used

6.    Consider adding a thin o-ring to seal LAF pucks in clamps\\]]></property>
<property name="content" class="Comment" package="com.atlassian.confluence.pages"><id name="id">10356450</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10389161</id>
<property name="body"><![CDATA[4.&nbsp; Investigate remaining puck handling problems warm and cold

&nbsp;&nbsp;&nbsp; a. still seeing Elbow errors even when Forearm not pressing puck against backstop&nbsp;

5.&nbsp; Add software check to stop if mission's start tube does not match last used

6.&nbsp;&nbsp;  Consider adding thin o-ring to seal LAF pucks in clamps




&nbsp; ]]></property>
<property name="content" class="Comment" package="com.atlassian.confluence.pages"><id name="id">10356449</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10389164</id>
<property name="body"><![CDATA[4.  Investigate remaining puck handling problems warm and cold

&nbsp; \-\- still seeing Elbow errors even when Forearm not pressing puck against backstop

5.  Add software check to ensure mission continuation's startTube matches last used

6.    Consider adding a thin o-ring to seal LAF pucks in clamps

7.&nbsp; Cool oil down to 3C and check its viscosity

8.&nbsp; Determine why sphere appears to be electrically connected to frame

9.&nbsp; Try to determine how much gas is dissolved on our silicon oil

&nbsp;&nbsp;&nbsp; \--&nbsp; we are seeing pressure increasing slowly during sampling
&nbsp;]]></property>
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<property name="body"><![CDATA[4.  Investigate remaining puck handling problems warm and cold

a. still seeing Elbow errors even when Forearm not pressing puck against backstop

5.  Add software check to ensure mission continuation's startTube matches last used

6.    Consider adding a thin o-ring to seal LAF pucks in clamps
\\]]></property>
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<property name="body"><![CDATA[Epoch secondswill be a floating point value.

In any case, keep in mind that the existing raw log file entry format is documented in ESP/gen2/software/lib/log.rb.&nbsp;

The one change I'm proposing is that the a single number with an optional decimal point shall be interpreted as

EPOCH SECONDS based from 1970 GMT (as you propose).&nbsp; I think the raw time entries must also allow an optional


time zone indicator suffix (PDT or PST, etc) .&nbsp; So, a raw log entry might look like this:

@12345.45PST`"Main"SNAP,phase=hab,start=1234939.77,file={{hires/bac08oct1716h450ml40s.tif,exposed=123.4}}

The timezone is "sticky".&nbsp; Once you see one, you should offset GMT times for the indicated zone until you see another.

This way I don't have to repeat them.&nbsp;

&nbsp;The backtick after time indicates the record type indicator is DATA.&nbsp; (again, see log.rb)

Strictly speaking, everything after the backtick until the end of the line may be defined any way you like


I like the&nbsp; key=value format, but try to keep the keys short (per my example above).&nbsp; This log file is too big as it is.

I kind of like the idea of units suffixes, if you really intend to parse them.&nbsp; But, if you are just going to ignore them,

I'd rather omit them entirely.&nbsp; That means, the data manager has to know that 1L == 1000ml

Are you up for that?\\]]></property>
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<property name="body"><![CDATA[Wanted to capture here from earlier GUI meeting discussions: ESP on-board will track and provide additional state items for things like number of pucks in a tube, capacity and current volume estimate for reagent & waste bags etc.&nbsp; These items can only really be inferred by the ESP as it is initialized and run as here is no sensor measuring these.&nbsp;&nbsp; ]]></property>
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<property name="body"><![CDATA[2-Feb-2011 There will be a keep-alive message at some interval for the case where nothing is changing in the subscribed-to states - so the dashboard can know when coms are lost with the esp.

3-Feb-2011 Roman pointed out that we also need to know at the dashboard when the the esp is locked up with an error. Rich discussed briefly with Brent. While it may not strictly be 'state',&nbsp; it is important info to communicate to users via the dashboard.&nbsp; Brent suggested perhaps a second socket would have the error messages (question... how then would we notify the dashboard when error condition had cleared?). ]]></property>
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